As I understand from your query, you have been employed by Company Y under whose policy, a notice of only 30 days is adequate. However, Company Y is a subsidiary of Company X under whose policy, a notice of 90 days is to be served and your employer is insisting that you serve a 90 day notice period in accordance with the Policy documents of Company X.
Since you are employed by Y and are an employee of Y, going by what is stated in the query, it prima facie seems like the policy framed and applicable to employees of Y that should apply to you. However, one might have to verify your appointment letter, the terms of the Employment contract if any and the HR policy of Company Y to see if the terms mentioned in the HR policy documents of Company X have been incorporated or given over-riding effect.
If, on examining the aforesaid documents it follows that you need only serve a 30 day notice period, you may categorically state so in your written Notice, referring to the relevant clauses of the HR Policy document.