A headspace sampler control system and a control method thereof belong to the field of gas phase chromatographic sample pre-treatment device control technology. The headspace sampler control system comprises a programmable controller, a temperature module, an analog quantity input and output module and man-machine interaction equipment. The programmable controller is connected with the temperature module and the man-machine interaction equipment. The temperature module is connected with the analog quantity input and output module. The programmable controller, the temperature module and the analog quantity input and output module are respectively connected with related components of a headspace sampler. The headspace sampler control system has advantages of high stability, high interference resistance, easy operation, easy maintenance, no requirement for welding of a main circuit board, convenient wiring and easy function expansion. Through a self-checking process for each key component of the headspace sampler, problem finding can be realized and a fault point can be found out directly. High control precision and simple operation are realized in a process for controlling temperature and pressure of a heating chamber, a valve and an air path. One-key sample incoming can be realized in an automatic control process for sample incoming of the headspace sampler. Operation time of an operator can be effectively reduced.