The present invention discloses an emergency clock synchronization method and system of an ultra-short base line positioning system. The emergency clock synchronization method includes the following steps that: the measurement depth of the ultra short base line positioning system, the measurement horizontal distance of the ultra-short base line positioning system and the true depth of a submersible are obtained; the positioning slope distance of the ultra-short base line positioning system and the true slope distance of the submersible and a water surface supported mother ship are determined according to the measurement depth and measurement horizontal distance of the ultra-short base line positioning system and the true depth of the submersible; the time delay difference of the synchronous clock of the submersible and the synchronous clock of the water surface supported mother ship is determined according to the positioning slope distance and the true slope distance of the submersible and the water surface supported mother ship; and a signal source is added to perform delay processing on synchronous signals outputted by the synchronous clock of the water surface supported mother ship, so that the time delay difference of the synchronous clock of the submersible and the synchronous clock of the water surface supported mother ship can be compensated, and therefore, the normal operation of the ultra-short base line positioning system can be ensured, and the precise positioning of the submersible can be realized.