The present invention discloses a helium ion gas chromatograph and a use method thereof. The helium ion gas chromatograph comprises a carrier gas source, a zero dead volume pressure stabilizing valve, a helium purification device, a zero dead volume four-way junction, a purging system inlet, a purging system outlet, a 5A molecular sieve chromatographic column, a detector, a back pressure valve and a sample device. The carrier gas source, the zero dead volume pressure stabilizing valve, the helium purification device and the zero dead volume four-way junction are sequentially communicated. Thezero dead volume four-way junction is respectively communicated with the purging system inlet, the detector and the sample device. The purging system inlet and the purging system outlet are arranged on the sample device. The sample device, the 5A molecular sieve chromatographic column, the detector and the back pressure valve are sequentially communicated. With the present invention, the interference of the background impurities in the carrier gas is eliminated, the interference to the system due to the air is eliminated, the detection limit of the sample is improved, the separation effect ofthe chromatographic column is improved, and the accuracy and the stability of the experimental results are improved.