The invention discloses a giant water turbine cylindrical valve synchronous control method based on three-level deviation protection. The opening and closing processes of a cylindrical valve are divided into a plurality of opening-degree sections according to the regulation speed, when the cylindrical valve moves to a certain opening-degree section, a controller automatic reads a regulation speedhistorical record chart, and a servomotor lowest in regulation speed in the current opening-degree section is inquired and set as the reference servomotor; in the cylindrical valve moving process, thecontroller works out the regulation speeds of all servomotors in the current opening-degree section in real time, and through comparison, the lowest servomotor is selected out; when the deviation ofthe servomotor exceeds the first deviation setting, the reference servomotor is automatically replaced and regulated; when the deviation of the servomotor exceeds the second deviation setting, reversemotion control is automatically started; and when the deviation of the servomotor exceeds the third deviation setting, the position of the servomotor is automatically locked. The giant water turbinecylindrical valve synchronous control method can start first-level deviation control, second-level deviation control and third-level deviation control in sequence according to increasing of the servomotor deviation value, the regulation criterion of synchronous control is dynamically regulated, reverse deviation rectifying and locking protection are automatically triggered, and the situation thatthe cylindrical valve steps out due to the fact that one servomotor breaks down is avoided.