Irrespective of the ownership of the company, you are employed in the UK and paid in the UK, even if part of your time is spent working working outside the UK. Your contract of employment is thus tied to the UK, and whatever it says in terms of notice is that which applies.
However you may be able to negotiate with your employer to get the 3 months reduced when you resign - it depends what you do and how they view you working out your notice. Best to keep the employer on your side - never know when you might need a reference.