about japanese naturalization

is it possible to apply for naturalization even i am separated but legally married in paper in my own country ?
i mean i have family in my country but were separated for many years..
and i have live in partner here in japan
i been living for 6 years in japan

What has one thing to do with the other?
If you have a valid residency status in Japan and are eligible to apply, you can apply.
If your residence status is based on being married to the person you haven’t seen in years, then that’s a different story, because then your current residency status is not really valid.

one of the conditions required is 素行が善良であること.
浮気, you have another partner in Japan, while you are married in your country, may be considered as 素行が善良ではない.
of course, you can tell a lie to pubic authorities. that is another 素行が善良でない and it is too risky.

divorce firstly will make the story easy.

You should understand that in the land of Japan, everything is 'paper' black and white.
Technically/Legally you are still married to your spouse (in your country) and that will be known and scrutinize by the authority when you try to apply for naturalization. They will require documentation on your life in your country.

Also, 'and i have live in partner here in japan' is irrelevant if it is not official, no proof/documentation.
And either they/authority consider that as normal 'friend' living together or 'cheating'/adultery(whether it is crime or not,who knows) BUT in term of character, as ken-san mentioned "Be of good moral character".....

No one can guarantee anything..you could try and apply, see if they accept your application. Do you have anything to lose ?

OP might be from a country that doesn’t allow for divorce. So if any question arises I’d mention that.
And as PP said, you have nothing to loose. If you get rejected you still have your current residence status.