A novel subsurface buoy data acquisition system, comprising: a battery compartment (1), a master control processor (2), a GPS receiver (3), a gigabit Ethernet interface module (4), and multiple data acquisition boards. The GPS receiver (3) is connected to the master control processor (2); the master control processor (2) is connected to an upper computer (6) by means of the gigabit Ethernet interface module (4); the data acquisition board comprises a hydrophone sensor (51), a front-end drive circuit (52), an AD conversion circuit (53), a clock module (54), a DA conversion circuit (55), an FPGA (56), an ARM processor (57), and a storage module (58); the hydrophone sensor (51) is connected to the AD conversion circuit (53) by means of the front-end drive circuit (52); the AD conversion circuit (53) is connected to the FPGA (56); the FPGA (56) is connected to the ARM processor (57); the storage module (58) is connected to the ARM processor (57); the DA conversion circuit (55) is connected to the FPGA (56) and the clock module (54); the clock module (54) is connected to the FPGA (56); and the ARM processor (57) is connected to the master control processor (2). The acquisition performance of a subsurface buoy data acquisition system is improved, and synchronous acquisition and control of the entire system are implemented.