In the modern radar signal environment, hybrid modulation signals are increasingly used in many systems. This study focuses on the Time Difference Of Arrival (TDOA) estimation problem of FSK-BPSK hybrid modulation signals. The method combines the characteristic of modulated signal and utilizes the sum of simple correlation functions of sub-pulses to elicit the complex correlation function of the entire pulse signal. Finally, a correlation function fitting algorithm is used to estimate the exact TDOA. Experimental results indicate an obvious improvement in the accuracy and noise immunity of the method, and the method is appropriate for the TDOA estimation of low-bandwidth hybrid modulation signals.