Are these sentences natural? 

There are two reasons.

Firstly, Kindai university is the most popular of all the Universities in Japan. 

Because the number of examinees is the largest in Japan for the fifth consecutive year. (Examinees is an acceptable word, but it is less confusing to say 'Students' instead.)

Secondly, Kindai university have has many good spots to study. in Kindai university. (No need to mention the subject, in this case Kindai university, twice)

For example, the English village, the library,  the computer room, the study room. 

So  These places help students of Kindai university can spend to have a comfortable and fulfilling campus life.

This sentence makes sense - the only issue is the word 'So.' At the beginning of a sentence, 'So' marks that the person using it is going to change the topic of discussion. To help this make more sense, it would be better to use something like 'these places help,' or 'these places allow.'

In conclusion, I think that Kindai university is the best of university. (No possessive preposition needed with superlatives)

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Everything you said here makes sense, but they are not quite natural yet. There is a lot you got right though, and the niceties of grammar come with time. Well done for that :)

Are these sentences natural?

There are two reasons.

Firstly, Kindai university is the most popular of all.

Because the number of examinees is the largest in Japan for the fifth consecutive year.

Secondly, Kindai University have has many good spots to study. in Kindai university.

For example, English village, library, computer room, and study room.

So students of Kindai University can have spend a comfortable and fulfilling campus life.

In conclusion, I think that Kindai University is the best of university.