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Forming a company does not factor into getting permanent residency in the Czech Republic.

Unless you get PR through marrying a Czech national or starting a family with them, you will need to accumulate 5 years of continuous visas and pass a basic Czech language test to apply for PR.

It is the Ministry of Interior who oversees immigration and residency matters. This is a link to their English page on applying for permanent residency, it will give you a start and contacts to the ministry if you wish to ask further questions:

Thank you so much for your advice. But forming a company there and after 5 year's I will get PR. Isn't it? or I understand wrong.

Forming a company doesn't affect PR. Forming a company will simply require you to get some different papers for the visa application that you would need if you were simply to be an employee somewhere.

PR is based on the total length of time you've been legally living in the country or by being married to a Czech. After five years of continuous, uninterrupted visas you will be able to apply for PR. Conversely, marrying a Czech can negate the waiting period.

I didn't have my own company until only a year before I got PR, I was a regular employee for the first four years I lived here. It never entered into my PR application at all.