The invention discloses an underwater structure detection robot control system and a motion control method. A water surface system comprises a water surface console, a water surface communication transceiver and an umbilical cable, and an underwater system comprises an underwater communication transceiver, a power supply unit, an embedded microcontroller, a power-propelled unit, a vision illumination unit, a motion switching unit, a safety protection unit and a sensor unit. Each function module is in a modular design, mounting and dismounting are convenient, the water surface console has an emergent stopping function, a wireless connection tablet personal computer is configured, movable monitoring can be achieved, communication modes are various, the data volume is large, the motion switching unit supports switching of two motion modes such as swimming and crawling, and reliable safety protection such as data storage and voltage and current detection can be achieved. By means of the underwater structure detection robot control system and the motion control method, the motion control method is based on a generalized prediction proportion integration differentiation (PID) control algorithm, system energy consumption can be effectively reduced, loads of components and parts are decreased, and a robot can be conveniently and stably controlled.