How does a non-California spouse’s income affect California taxes of the other spouse who has only California income (Form 540NR)?

These are the Form 540NR instructions for these lines:

Line 36 – CA Tax Rate

In this computation, the FTB rounds the tax rate to four digits after the decimal. If your computation is different, you may receive a notice due to the difference in rounding. Contact us at 800-852-5711 if you disagree with this notice.

Line 38 – CA Exemption Credit Percentage

Divide the California Taxable Income (line 35) by Total Taxable Income (line 19). This percentage does not apply to the Nonrefundable Renter’s Credit, Nonrefundable Child and Dependent Care Expenses Credit, Other State Tax Credit, or credits that are conditional upon a transaction occurring wholly within California. If more than 1, enter 1.0000.

California income tax rate tables are here, and California income tax schedules are here.

To your questions:

Does California use your total federal income (including non-CA income) to determine your California tax rate, even though you're still only taxed on the CA-source portion?

Yes, see instructions linked above to line 31 and 36.

And does California require you to prorate exemptions and credits based on the ratio of CA income to total income?

Yes, see the instructions above.

Is there anything that prevents couple to file jointly at federal level and then separately at California? If husband and wife have separate property agreement matter here?

The instructions linked above say:

Use the same filing status for California that you used for your federal income tax return, unless you are an RDP. If you are an RDP and file single for federal, you must file married/RDP filing jointly or married/RDP filing separately for California. If you are an RDP and file head of household for federal purposes, you may file head of household for California purposes only if you meet the requirements to be considered unmarried or considered not in a domestic partnership.

Exception: If you file a joint tax return for federal, you may file separately for California if either spouse was either of the following:

• An active member of the United States armed forces or any auxiliary military branch during 2024.
• A nonresident for the entire year and had no income from California sources during 2024.

Community Property States: If the spouse earning the California source income is domiciled in a community property state, community income will be split equally between the spouses. Both spouses will have California source income and they will not qualify for the nonresident spouse exception.

Second exception might apply to your scenario if you have a valid property agreement overriding Texas and California community property rules.