This paper describes a control algorithm for the buffer of a deep-sea mining system, in which the buffer is connected to a long slender pipe and then to a surface ship on one end, and to a collector on sea floor through a flexible hose on the other end. A mathematical modeling is established for designing the controller for buffer thrusters, in which the dynamic response of the long pipe is taken into account based on the mode superposition method. The fluid loading acting on the pipe is estimated by using Morison`s formula. For simplicity, the surface ship is assumed to be kept stationary, the reaction from the flexible hose is ignored and only the lateral motions are considered. In order to guide the buffer to react only to the low-frequency motion of the surface vessel, the FIR digital filter is introduced to a PID-based controller It can be shown numerically that the high frequency component of the ship`s motion can be effectively filtered out by using the FIR low pass filter.