Hello.

I have old website with very complicated navigation, now I am changing urls to the new one using 301 redirect. Its long to explain, but basically is it ok if there will be 2 redirects?
Like
Old_url => another possible old url => new one
?

Also another question.
I have a lot of pages in sitemap, all of them will change their urls - how google will react on it? I mean, it may consider so much new pages as spam and set some penatly for site?

Nope; use a single redirect

It can take several months for one to take effect, with two it could take forever.

how google will react on it

Eventually it will crawl the new pages.

yah, single redirect will do.