Can anyone help me with this grammar structure?

1. The university, where over ten thousand students are studying, consists of seven faculties, two educational centers and thirty-nine departments.

* You need a comma before "where." "Where" begins an nonrestrictive clause. If you leave the comma out, you are making it restrictive by implying that there are a number of universities with various numbers of students but that the one of that group you are talking about is the one where over ten thousand students are studying. However, when you put the comma in, it means that you are talking about only one university, not one of a group, and that the university has more than ten thousand students, which is clearly what is meant within the given context, so commas should be placed on either side of the clause to make it nonrestrictive.

* Spell "ten thousand" rather then write, "10,000." When it comes to numbers, normally we write whole numbers 10 and above as numerals, which would make you believe you should write, "10,000." However, when the number being referred to isn't an exact number but being used in a phrase to approximate a number, then grammar requires you to write the number out as words. Since you aren't saying there are exactly 10,000 students but some approximate amount just over ten thousand students, you must write, "ten thousand," as words instead of numerals.

* Since seven is a whole number from zero through nine, the word "seven" should be written out as the word "seven" and not as the numeral "7."

* Since two is a whole number from zero through nine, the word "two" should be written out as the word "two" and not as the numeral "2."

* While 39 is a number 10 or above, it still must be written out as words despite the rule that says otherwise. The reason is that when numbers are in a list, the rule is to keep them all consistent, even if it means overriding the rule that would write it otherwise. Since the two preceding numbers in the list, seven and two, were written out as words, the rule then becomes to write "thirty-nine" as words to stay consistent with the list rather than as "39" as we would otherwise do.

* The comma after "studying" MUST remain. This comma should NOT be deleted. The comma signals the end of the nonrestrictive clause that started with the comma required before "where."

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2. The university consists of seven faculties, two educational centers and thirty-nine departments where over ten thousand students are studying,

* There should be no comma after "university." A comma should never separate the subject (university) from the verb (consists) of a sentence.

* I won't go into explaining the grammatical rules for writing numbers again. Just see above.

* Remove the comma before "where." "Where" starts a subordinate clause. This same clause was separated from the main clause by commas in the first sentence because the clause preceded the verb in the main clause. However, trailing the main clause, it should not be separated from the main clause by a comma. Its position away from the subject makes the clause automatically nonrestrictive, so it does not need to be set apart by commas to so designate it as it did before.

They're both correct, but #1 is clearer.

Also, remove the comma after "studying" --
The university where over 10000 students are studying consists of 7 faculties, 2 educational centers and 39 departments.

OR: Add a comma after "university" --
The university, where over 10000 students are studying, consists of 7 faculties, 2 educational centers and 39 departments.

The version you use will depend on whether you want to treat the phrase "where over 10000 students are studying" as parenthetical or not. If it's incidental to the main thrust of your statement, then it's parenthetical and needs commas before and after. If it's a significant point in your statement, then it's not parenthetical and you should not use any commas.

But in this type of construction, you must never use only one comma. If you use a comma to open a phrase, you must use a comma to close it. Likewise, you cannot close a phrase with a comma unless you had already opened it with one.

1. This one is the better one. There is nothing really incorrect with sentence 2, but sentence 1 is better. This is why:
You have said that there are over 10,000 students who are studying at the university. In sentence 2, "...where over 10,000 students are studying," is placed too far away from "The university..." "...where over...studying" should be placed as close as possible to the place where they are studying, namely, "The university..." That is why sentence 1 is the better choice. By the way, there should be a comma in sentence 1 after "university".