What should I do if doxycycline is not working for my acne?

It may be because your acne is severe and hence may need stronger treatment like isotretinoin. Another reason is non-compliance or you have not tried doxycycline long enough (usually takes 2-3 months to see significant results). Perhaps your acne is hormonal driven (in females), hence an oral contraceptive may be more beneficial for you. I would advise you to see a dermatologist for further assessment.