Rapid and correct detection of harmonics is the premise of suppressing harmonics in power system, and is also of great significance to the improvement of power quality. A new detection method for the harmonics based on a modified S-transform (MST) is proposed, in which three parameters of p, q and λ are introduced into the Gaussian window function in conventional S-transform (ST). According to the differences of the input signal, suitable parameters of Gaussian window are selected to extract the characteristic quantities of harmonics such as harmonic order, amplitude, and the start and end time of transient state, etc. The fundamental principle and characteristics of the MST are firstly presented, and then the detection method of harmonics in power system based on MST is elaborated in detail. Finally, the steady harmonics, transient harmonics and the harmonics with noise are simulated respectively. The simulation results verify the efficiency of the proposed method, and show that it is also characterized by simple utilization, high accuracy, and good anti-interference performance. Furthermore, the method can be also used for the detection of the power harmonics under the condition of low signal noise ratio (SNR).