Thermal conductivity is one of the important parameters of microbolometer pixels, and its magnitude directly affects the response of the pixel. Thermal conductivity is related to the thermal conductivity of the thin film materials that make up the pixels. The characteristic size, temperature, and deposition process of the thin film all affect the thermal conductivity. Monitoring the thermal conductivity of thin films on the production line is of great significance for the design of pixels. Based on the 3ω harmonic detection technology, a testing system for the thermal conductivity of thin films was built, and the thermal conductivity of SiNx and SiO2 thin films with a thickness of 20～100 nm was tested, including temperature and dimensional characteristics. According to the dimensional characteristics, the intrinsic thermal conductivity of SiNx is 0.747 W/(m·K), and that of SiO2 is 1.085 W/(m·K). The thermal conductivity of a titanium film with a thickness of 100 nm was tested to be 6.708 W/(m·K). Compared with the testing system based on photo-thermal method, the construction of the 3ω method testing system is simpler. This method utilizes the manufacturing process of micro-electromechanical systems (MEMS) to prepare test samples, which is an ideal solution for characterizing the thermal conductivity of micro-nano scale thin films in MEMS product design and manufacturing.