Perfect Blue is one of my favorite movies, which was directed by sSatoshi kKon, a well-known Japanese anime filmmaker, is one of my favorite movies.

You could also split this into two sentences.
"Perfect Blue is one of my favourite movies. It was directed by Satoshi Kon, a well-known Japanese anime filmmaker."

I had watched it several times back in university and I was totally entranced by the intricate plots in thise film that tells a story that mingles both the dream and reality of a Japanese idols’s life.

Because it says "reality of A Japanese idol" --> it is singular! So we change "idols' " to "idol's"
You can also rewrite this sentence to be a bit more clear
ex) "..by the intricate plot. The film tells a story that merges/explores(?) both the dream and reality of a Japanese idol's life."

sSince the film was shown in 1997, the various analyses about this film werehave been blooming till now because of the opening ending.

Instead of "blooming" using "discussed, created" could be more clear. You could also write it as "...about this film are still arising/being discussed today..."

Like the saying “there are a thousand hHamlets in a thousand people’s eyes”, people ownshave different views about this film that makes it unfading.

Instead of "that make it unfading" --> "that keep it relevant" or "that keep it everlasting/unending" are also other ways to phrase it

Perfect Blue is one of my favorite movies which, it was directed by satoshi kon a well-know Japanese anime filmmaker.

"One of my favorite movies which was directed by Satoshi Kon" makes it sound like "among Sotoshi Kon's movies, this is one of my favorites." Rather, given that the title is "one of my favorite movies", I assumed you meant among all movies, not just Sotashi Kon's works.

I had watched it several times back in university and I was totally entranced by the intricate plots in this film that tells a story mingles both dream and reality of a Japanese idols’ life.

Had: "I had watched it several times by the time I graduated" would be fine I think, but I can't really explain why it feels wrong here. Roughly, I think if you're talking about a point in time in the past, T, and something happened prior to T, you say "by the time T happened, it HAD already happened",

since the film was shown in 1997, the various analyses about this film werhave blooming till nowed because of the opening ending.

Like the saying “there are a thousand hamlets in a thousand people’s eyes”, it is people's owns different unique views about this film that makes it unfading.

"People's views about the film prevent it from fading" would work by establishing "people's views about the film" as the subject and the verb becomes "prevent". However, "people own different views about this film" is already a complete sentence so you need a conjunction like "so".