The invention relates to a deviation rectifying control system and a deviation rectifying control method of a crane. The system comprises a main frequency converter, a slave frequency converter, a first position sensor and a second position sensor, wherein the main frequency converter and the slave frequency converter are respectively used for controlling a rigid leg and a soft leg of the crane to move, the first position sensor and the second position sensor are arranged on end beams on both sides of the crane and respectively used for obtaining position signals of the end beams on the both sides, and the main frequency converter is used for calculating real-time position deviation of the end beams on the both sides according to the position signals of the end beams on the both sides of the crane, calculating the output frequency of the slave frequency converter according to the real-time position deviation and the set frequency of the main frequency converter and outputting the output frequency to the slave frequency converter for executing, so as to reduce the real-time position deviation of the end beams on the both sides. According to the system, the position signals which are collected by the position sensors on the end beams on the both sides can be directly obtained by the main frequency converter, and the real-time position deviation is calculated to perform deviation rectifying control. Compared with the deviation rectifying control by virtue of a PLC (Programmable Logic Controller) in the prior art, the system has the advantages that the electric control cost can be reduced, and the real-time performance of signal transmission can be improved.