The invention provides a high-throughput satellite communication system beam hopping method. According to the method, uniform clustering is carried out on total beams according to a business requirement, an objective function is established for the requirement, whether edge beam distance of adjacent clusters is equal to 2R and the same are in working status is monitored, if not, performance satisfies direct calculation of frequency spectrum efficiency, and if yes, an interference avoidance measure is taken, then the frequency spectrum efficiency is calculated, a KKT condition is used for solving of time slot allocation numbers of a closed-form solution, finally, rounding-down is carried out according to values of the closed-form solution, the same is optimized, and optimal capacity allocation is obtained. The method has the advantages that a dynamic requirement of capacity can be satisfied, frequency spectrum efficiency can be improved, and performance decreasing caused by interferenceof the same frequency can also be avoided.