The invention discloses a channel main floating body and supporting floating body coupled water surface photovoltaic power generation system and a method thereof. The system is obtained through splicing a plurality of photovoltaic power generation units. Each photovoltaic power generation unit comprises two main floating bodies and an assembly supporting floating body. Two end surfaces of each main floating body in the length direction are respectively provided with a high spacing board and a low spacing board. The assembly supporting floating body is a cube with an open top surface. Two end surfaces of the assembly supporting floating body are arc-shaped surfaces. Two side walls of the main floating body in the width direction are provided with recessed surface which match the arc-shaped surfaces. Two ends of the top of the arc-shaped surface at one end of the assembly supporting floating body are provided with high vertical columns, and two ends of the top of the arc-shaped surface at the other end of the assembly supporting floating body are provided with inverted-L-shaped pressing blocks. The high vertical columns and the inverted-L-shaped pressing blocks are provided with photovoltaic assemblies. The channel main floating body and supporting floating body coupled water surface photovoltaic power generation system and the method thereof have advantages of reducing strength requirement to the assembly supporting floating body, simplifying the manner of the assembly supporting floating body, reducing fabrication cost, improving integral stability of the water surface photovoltaic power generation system, reducing vibration amplitude of the photovoltaic assemblies, and increasing power generation amount.