I started to watch Naruto and I didn’t read the manga. Some people told me that they have so many differences and its even like a separated version. Why is it like that? I searched it on Google but couldn’t find anything.
Yes, there are indeed some differences, but to call it a separated version? I think not.
In most anime, 1 episode tries to cover around 2-5 chapters of the manga. Quite often there is too much information or things going on in the chapters to properly cover in 1 episode of ~19 minutes. This means they have to 'cut down' some of the manga's content. Cutting the content as such often leads to lacking some build up, or additional information. Which, especially if you did read the manga before, makes it feel like a whole different story. Or a lacking story.
Besides these differences, Naruto also features quite a few fillers. As Aki Tanaka mentioned in the comments as well: Which episodes of the Naruto anime are core plot and which are filler?
However, those fillers can be considered as additional content, as this does not replace content. But more about that is explained in Why make filler episodes?