The disclosure discloses a method and a system for scheduling frequency physical resources based on frequency hopping. The method comprises: in two time slots of frequency hopping transmission, reserving frequency physical resources for an activated semi-persistent scheduling new transmission user with a transmission period reached and a retransmission user; obtaining a scheduling type of a user required for scheduling, and according to an occupancy situation of the frequency physical resources, obtaining corresponding available frequency physical resources when employing a frequency-selective scheduling type and a non-frequency-selective scheduling type; and according to the scheduling type of the user required for scheduling, searching for corresponding available frequency physical resources, and allocating the frequency physical resources to a frequency-selective scheduling user and a non-frequency-selective scheduling user simultaneously during one scheduling period. The disclosure comprehensively utilizes advantages of the frequency-selective scheduling and non-frequency-selective scheduling, so that the users with good channel quality can utilize the frequency-selective scheduling to obtain the optimal frequency resources, the users without channel quality information can obtain frequency diversity gain through frequency hopping, and the system capacity can be improved without increasing equipment costs.