The invention relates to an automatic gas sample collection station for monitoring greenhouse gas emission flux. The collection station comprises a power system, a master control system, an automatic static box, a water seal system, an automatic static box lifting system, a gas collection system, a gas injection system, a positioning system and a sample disc collection system. The main operating processes of the station comprises the following steps: supplying power through the power supply, sequentially controlling the covering of the box, the adding of water and sealing, collecting of gas, positioning of a sample bottle and injecting of gas through the master control system and recording environmental conditions during gas collection. After the gas sample is completely collected for the first time, the automatic static box is controlled to open, and sampling starts again when the next sampling time reaches. The master control system can transmit instructions through field key operation and also can be remotely or wirelessly controlled to operate or transmit a status report. The automatic gas sample collection station is mainly used for fully automatically sampling and monitoring greenhouse gases emitted from agriculture, forestry, grassland and natural ecosystem environments and also can be used for automatically sampling gases during atmospheric environmental monitoring.