The key of on-line monitoring of dissolved gas in transformer oil is the sensor technology of gas detection, in which how to accurately measure and analyze the content of carbon dioxide in oil is the technical difficulties. To solve this problem, this paper designs a thermal conductivity detection system based on rectangular window time-domain filtering algorithm. The system uses a new thermal conductivity sensor TCS208F, utilizes the combined method of analog and digital filtering for its small output signal and difficult issues in signal acquisition and analysis. Finally, this paper completes the optimum design of hardware and software of thermal conductivity detector system, realizes the collection and analysis of weak signal of carbon dioxide gas. This method effectively suppresses the noise of various types, improves the accuracy and sensitivity of system measurement, achieves the accurate measurement of trace gas concentrations, and overcomes the shortcomings of traditional gas thermal conductivity detection.