The invention provides a relay satellite mission scheduling method and system, and relates to the technical field of relay satellites. The method comprises the following steps: setting scheduling initial information, and acquiring at least two pieces of mission information; respectively calculating greedy function values of the at least two pieces of mission information; sequencing the greedy function values to obtain a mission sequence corresponding to the greedy function values, and establishing a mission constraint candidate list according to the sequence; updating antenna pointing path information according to the mission constraint candidate list; and acquiring a feasible solution for relay satellite mission scheduling based on a constraint condition of the antenna pointing path information. According to the relay satellite mission scheduling method provided by the invention, the technical problems of unreasonable preparation time distribution, waste of antenna time resources andinfluence on the relay service quality which are caused by the reason that the relay satellite scheduling system reserves the longest and same mission preparation time for all users are solved, and atechnical effect of optimizing the relay satellite mission scheduling is achieved.