The invention discloses a treatment system for aquaculture wastewater with a low carbon-nitrogen ratio and a wastewater treatment method and belongs to the technical field of biological wastewater treatment. The treatment system comprises a nitrification device, a denitrification device, a wastewater storage device, a pipeline and a circulation pump, wherein the nitrification device and the denitrification device are connected together; the pipeline is used for communicating; the circulation pump is used for making the wastewater flow in the device in cycle; the treatment method comprises the steps of (1) biofilm culturing, (2) circulating treatment, and (3) repeating. The wastewater treatment system and the wastewater treatment method are suitable for treatment of aquaculture wastewater with the low carbon-nitrogen ratio; a biofilm formed by bacterial communities can be formed on a filler; the removal rate on ammonia nitrogen, nitrite nitrogen and total nitrogen basically can be kept over 90%; the system is stable in operation, free of secondary pollution, convenient to maintain and easy to operate.