My answer would be yes, as long as it was rolled during an official league and you do pay for your sanction in a timely manner it will count. You should check with the President or VP of your league though as it is up to them to enter your honor score(s) with the USBC.

My league isn't paying for sanction until at least week 2 because the USBC is late getting the cards to the league.  I'm sure this won't impact any scores rolled during the first two weeks.

first day of league and roll an honor score. but didnt pay the sanction fee  (paid  the following week ) . will that honor score be reconized by USBC

I think that honor point is not recognized by USB. In my opinion, you should check with the President or Vice President to get the most accurate answer.