Yes with the Online version you would need 2 accounts and pay twice. So buy the Desktop CD/Download program
https://turbotax.intuit.com/personal-taxes/cd-download/
And may I ask why you are filing separate returns? Sometimes people don't realize the differences between filing Joint and MFS.
Unless you have a specific reason to file separate returns,
It is usually better to file Joint. Joint has the lowest tax rates and the highest Standard Deduction. And if you are in a Community Property state MFS gets tricky to figure out. Here's some things to consider about filing separately……
In the first place you each have to file a separate return, so that's two returns. And if you are using the Online version that means using 2 accounts and paying the fees twice.
Many people think they come out better when filing Married Filing Separate but they are probably doing it wrong. If one person itemizes deductions then the other one must itemize too, even if it's less than the standard deduction, even if it is ZERO!
And there are several credits you can't take when filing separately, like the
EITC Earned Income Tax Credit
Child Care Credit
Educational Deductions and Credits
And contributions to IRA and ROTH IRA are limited when you file MFS.
Also if you file Married Filing Separately up to 85`% of your Social Security becomes taxable right away even with zero other income.
See …….
Yes, you would need and pay for two accounts if both you and your spouse are going to file tax returns as Married Filing Separately and use the TurboTax online editions.
Or you can purchase one of the TurboTax desktop CD/Download editions and create two tax returns at no charge after purchasing the software.
See this TurboTax support FAQ for filing jointly versus separately - https://ttlc.intuit.com/community/married/help/is-it-better-for-a-married-couple-to-file-jointly-or-separately/01/25590