My W-4 is filled as single, but I'm married

[LCM2]

My former employer have filled my W-4 as a single non-resident alien.

However, I am married and considered a resident alien for tax purposes (substantial presence test). My spouse is also considered resident alien.

Will I have any problem with IRS if my spouse an I file our taxes as Married filling jointly?

[DoninGA]

No, there will not be a problem with the IRS.  What the status is on your W-4 has no bearing on the filing status you use on your federal tax return.

[xmasbaby0]

The W-4 you gave your employer affects the amount of tax the employer withholds from your paychecks.  It does not dictate how you have to file your tax return.   You simply had tax withheld at the "single" rate, which does not prevent you from filing as married.