My sister left her 4 years old son in the care of my parents for days now we don't know where she is and did not contact us, the child is an illegitimate,my parents and I are the one who provide the child's education,medical needs,food,clothing since birth,how can we file custody for the child In case my sister will come back and get her son?

Illegitimate, people still use that word? That has no bearing on the father having legal rights, So any attempt at custody has to include legal notification of both the mother and father of the child.

You will need hire an attorney, since this will be a complicated issue, and decide what is best way to proceed.

Start with applying for temporary guardianship, which is easier. This gives you the legal right to care for the child. Then you will need an attorney to go for custody.

Illegitimate, people still use that word? ...

It's perfectly good word, but misused by the OP (it's an adjective, not a noun). Would you rather use "bastard"?

I suspect that what OP should do depends on the law in the Philippines. I don't really know how it works there.