How should i file my income tax return? I am a resident Alien, married last march 2024 in the Philippines. my spouse is NRA with no income.

Because you are married, you will have to file your tax return married- separate or joint.  You will need to get an ITIN for your spouse.  Because she has no income, you may benefit from filing joint and treating her as a resident alien.  See Nonresident alien spouse treated as a resident alien and Taxpayer identification number requirement.

So what if I don't want to consider him as a resident alien ? Which is better to consider that he is Resident or NRA ? Is this will affect on his ongoing petition ?

Non-resident alien doesn't become a deduction for you but resident alien does.  

Not sure if filing taxes as a resident or non-resident alien helps with the citizenship application.  That is a question for your attorney.

@christinebarangan