Strictly uniform time interval between adjacent channels is a crucial requirement for the multi-wavelength interleaved (MWI) pulse sources, which difficult alignment can be easily solved by what we believe to be our novel method based on frequency-resolved optical gating (FROG). By utilizing highly precise measurements from FROG, which provide fully two-dimensional information of the pulses in time and frequency domain, we can intuitively identify the time mismatches between different channels in the MWI pulse sources. This enables us to directly align the timing of each channel with sub-picosecond resolution at the first time. MWI pulse sources with total repetition rate of 20.8 GHz (four wavelengths) and 41.6 GHz (eight wavelengths) are precisely aligned by the proposed method, this achievement will pave the way for advancements in photonic analog-digital converters (PADC), high-speed optical communications and so on.