This paper addresses a new method of parameter estimation for hybrid DS/FH_BPSK signals based on S transform(ST) with an asymmetrical window. Good performance is achieved by two stages. Firstly, a nonlinear process is used to produce the reference signal(RFS) which has the same hopping parameter as the original signal. Then S transform is improved by using an asymmetrical window instead of a Gaussian one and the ridge curve of ST is extracted as the instantaneous frequency of RFS. This asymmetrical window has a sharper taper in the forward direction and a compensating slower taper in the backward direction. Thus the resolution of hopping termination times is sacrificed to improve the resolution of hopping initiation time in the resultant time-frequency spectrum. Since the onset and the offset of every hopping can provide the same parameter information, the asymmetrical S transform is better at parameter estimation for hybrid DS/FH spread spectrum signals than that which uses the symmetrical windows. The simulation results show that the proposed method can operate effectively for hopping parameter estimation.