The invention relates to a method and apparatus of controlling switch valves in a sequence control system, relates to the sequence control field, and is mainly aimed at simplifying conditions input by users and minimizing input errors. The adopted main technical scheme is that the method of controlling switch valves in a sequence control system, used for controlling on and off of multiple switch valves, includes the following steps: inputting a decimal number into a converter; the converter converting the input decimal number into a binary code, wherein the digit number of the binary code is equal to and corresponds to the number of the switch valves; and converting the values of the binary code in all digits into signals, wherein each signal controls on and off of one switch valve that corresponds to the corresponding digit. A user can achieve a unified control over the multiple switch valves in sequentially controlled separate steps only by inputting a decimal number into the converter. Therefore, conditions input by the user are simplified, and input errors by the user are minimized.