In order to measure the distribution of carbon dioxide (CO2) concentration gradient in farmland accurately, and reduce the interference error caused by manual measurement, a CO2 concentration gradient in-situ synchronous measurement system was designed, which was equipped in farmland to measure CO2 concentration gradient automatically, and the measurement data could be sent to the host computer server via GPRS wireless transmission technology. The system was composed of a mechanical collection module and an electrical control module. The mechanical acquisition module was responsible for the gas collection, and the system control module was used to realize the automatic measurement of CO2 concentration. The overall structure of the measurement system and the design of each module were introduced, and the pumping process of carbon dioxide measurement was simulated by computational fluid dynamics (CFD) software. The relationships between the distance of the measurement pipeline and the pumping speed, as well as the diameter of the pipeline were analyzed to optimize the system design. The indoor system calibration and outdoor field measurement of carbon dioxide concentration were implemented. The experimental results showed that the system could measure the concentration gradient of farmland carbon dioxide, and the measurement error was not more than 4.17%. The system could realize the automatic acquisition of cropland information, which had important significance to the carbon sequestration information calculation.