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.