This paper introduces a special drill machine for machining flange hole. Base on design project Specifications, discussed system compose and machining requirement. Design actuator and hydraulic system. The electric control system chooses programmable controller, according to the logic relation of processing request, design control programs with the sequence function chart, analyzed the processing cycle technological process. Point out that using the sequence function chart to design special drill machine control programs, it is logical and adaptable and also convenient on changing the programs. The programmable controller is just designed for industry control, so it is reliable and anti-jamming.