In the transmission process, broadband optical pulses generated through sinusoidal phase modulation, as a result of changes in spectral composition, will lead to FM-to-AM, resulting in pulse intensity modulation in the time domain. It is difficult to measure the microstructure of spectrum accurately due to the narrow spectrum bandwidth (about 0.3nm). In order to control this effect, the paper presents a compensation method of spectral shaping guided by waveform measurement. By measuring the waveform before and after transmission, the shaping pulse spectrum will be calculated using G-S iterative method. Liquid crystal spatial modulator is used for spectrum shaping in order to compensate FM-to-AM effect. By numerical simulation, the details of the methods are improved and requirements for measuring instruments are proposed. The results show that, under certain transmission conditions, this method can effectively control the FM-to-AM effect, to resolve the issue of time-domain intensity modulation.