The invention provides primary frequency modulation control method and system of a new energy power station. The primary frequency modulation control method includes: calculating active power output regulating variables and new active power reference values on primary frequency modulation of the new energy power station; evaluating active power output margins of power generation units in the new energy power station; calculating the active power output regulating variables of the power generation units according to the active power output margins; according to the new active power reference values and the active power output regulating variables of the power generation units, calculating the active power reference values of the power generation units, and the power generation units performing active power output according to the active power output values. Compared with the prior art, the primary frequency modulation control method and system has the advantages that both the active power output regulating variables of the new energy power station and the active power output margins of the power generation units are taken into consideration, and grid-connection frequency of the new energy power station can be regulated under the premise of safe operation of the power generation units.