No not necessarily.
Although you are stationed in SC, if she is a resident of NY, then she will need to file an NY residency state income tax return (regardless of where you are stationed or if all of her income was earned in SC). So as an NY resident, she will be taxed on all income from all sources (including any SC-source income).
If she qualifies under the MSRRA
and NY is also your
home of record, then you can file this NY resident return jointly. (No SC state income tax return would be required).
If she is covered by MSRRA and did end up with SC withholding on her W-2,
she will have to file an SC nonresident state income tax return to get these
SC withholdings back.
In
order to get the full refund of her SC state income tax withholdings, she will
need to file a nonresident SC return but report zero "0" income from
SC (even though she did have SC wage income). She must mail in this SC
nonresident state income tax return and include her state W-2 information. She
will want to include an explanatory statement with her SC nonresident state
income tax return stating her situation (that her SC employer withheld SC
state income taxes from her wages in error because she is a military spouse and
covered under MSRRA).
However, if she has SC earnings and is not covered under MSRRA then she will need to do both an SC nonresident state income tax return and a NY resident state income tax return. She will get a state income tax credit in NY for any income that is taxed in both SC and NY.
In
this instance (if she is not covered under MSRRA), you would still be able to file your federal income taxes
jointly but you would need to file your state income taxes as married filing
separately.
https://ttlc.intuit.com/replies/3301995
https://ttlc.intuit.com/replies/3302300
