The invention provides a pulse arrival timestamp marking method based on secondary zero crossing point detection and judgment. According to the method, a time synchronization-based time difference measurement principle is adopted, each of a main station and various secondary stations sets a high-stability and unified time reference, receives a target response signal, detects, judges and digitalizes the target response signal, searches for a signal crossing point, marks a time stamp and acquires the time of arrival of the target response signal, and the main station and the various secondary stations calculate the time of arrival of the target response signal according to the respective time stamps and then transmit the time of arrival to a data processing center; and the data processing center calculates the time difference of arrival according to the time of arrival, and then the position of a target is estimated. The method has the advantages that the time deviations between the marking positions of the time of arrival and the correct time of arrival (the zero crossing points) can be minimized maximally, the purpose of suppressing time of arrival estimation errors caused by zerocrossing point detection is achieved, and the precision of TOA measurement of the base stations can be significantly improved in the environment which is bad in signal-to-noise ratio.