The invention belongs to the field of water area monitoring, in particular to a multi-base station type water area monitoring control system and a monitoring control method thereof. The multi-base station type water area monitoring control system comprises a multi-base station target data fusion system, an electronic chart system, a ship control system, a video monitoring system, a video transferservice system, an AIS base station and a water area multiple joint cognitive base station; the multi-base station target data fusion system firstly fuses multiple paths of radar target data to obtaina path of radar target data, and fuses a path of radar target data with AIS data to obtain track target data, thereby greatly reducing the negative influence caused by sea clutter and improving the target measurement precision. If the optoelectronic device cannot perform accurate evidence extraction, an unmanned aerial vehicle is called to perform onsite snapshot evidence extraction, so that theship management reliability is greatly improved.