Can i check in my luggage in shekou port ferry? My airline is Cebupacific air to Manila?

I am sorry that you cannot check in your luggage at the port.

Thanks for your reply Betty. How about for Philippines Airlines?

I plan to take a ferry from this port to HKIA. May I know why cannot take it because my Airline is Cebu pacific?

Neither can Philippines Airline passengers check in their luggage at the port. These airline passengers can check in their luggage at the port: Japan Airlines, Cathay Pacific Airways, EVA Air, Dragonair, China Airlines, Garuda Indonesia Airlines, Hong Kong Airlines, Mandarin Airlines, Air Canada, Mega Global Air, Air India, Air Astana, Jestar Japan, Jet Airways, Thai Airways, Air China, Spring Airlines, Emirates Airline, Sibir Airlines, Virgin Atlantic, Etihad Airways, and Myanmar National Airline.

Thanks for the info, if my understanding is correct i cannot just check in my luggage but I can take the ferry to HKIA spypier? Is my understanding correct?

Yes, you are right.
It's ok for you to take the ferry at the port. But you cannot enjoy the check-in service in this port. You need to check-in at the airport. :)