I will fly from Bangkok to Beijing with Air China and connect to BJ to Frankfurt with Lufthansa. Baggage is checked through, however is a Visa needed (Thai passport holder)?

If you just make an international transfer in the airport without going out, the visa is not needed.
I only know, the check-in counter is in E area in T3, but not very clear about the transit counter. It is suggested to ask them directly and the phone number is 010-64598866.