A fast time synchronization method for large-scale LEO satellite networks based on a bionic algorithm is proposed. Because the inter-satellite links are continuously established and interrupted due to the relative motion of the satellites, the topology of the LEO satellite networks is time varying. Firstly, according to the ephemeris information in navigation messages, a connection table which records the connections between satellites is generated. Then, based on the connection table, the current satellite network topology is calculated and generated. Furthermore, a bionic algorithm is used to select some satellites as time source nodes and calculate the hierarchy of the clock transmission tree. By taking the minimum level of the time transmission tree as the optimization objective, the time source nodes and the clock stratums of the whole satellite networks are obtained. Finally, the onboard computational center broadcasts the time layer table to all the satellites in the LEO satellite networks and the time synchronization links can be established or recovered fast.