Provided are a hardware-in-loop simulation method and system. The hardware-in-loop simulation method comprises the steps of obtaining the detection amount output by an electric power system model when the hardware-in-loop simulation system runs in a stable state; obtaining the total delay time of the hardware-in-loop simulation system and obtaining power-frequency periodic time; calculating the delay point number according to the total delay time, preset power-frequency period sampling point number and the power-frequency periodic time; performing quick disperse Fourier decomposition on the detection amount to obtain a solid portion and an imaginary portion; performing phase compensation on the solid portion and the imaginary portion according to the delay point number to obtain a compensated solid portion and a compensated imaginary portion; combining and superposing the compensated solid portion and the compensated imaginary portion through disperse Fourier inversion to obtain compensated detection amount; performing a loop simulation test on an electrical device to be detected according to the compensated detection amount. By means of the scheme, the simulation stability and accuracy of the hardware-in-loop simulation system are improved, and meanwhile the cost is low.