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To meet the need for high-precision frequency measurement in gas detection using Quartz Crystal Microbalance (QCM) sensors, a high-precision frequency measurement system based on FPGA is designed. A method of equal-precision frequency measurement based on phase-locked loop is proposed, reducing the theoretical relative error of frequency measurement. The overall architecture of the frequency measurement system is designed, and based on this architecture, the hardware circuit of the high-precision frequency measurement system using FPGA is completed. An embedded software is also designed, which includes modules for frequency measurement, communication, and firmware programming. This software enables the integration of the high-precision frequency measurement system based on FPGA and its application in carbon dioxide gas concentration detection using QCM. Experimental results show that the absolute error of the frequency system measurement does not exceed 0.35Hz, with an average error of 0.268Hz and a maximum relative error of 3.5×10^-8. The frequency measurement resolution can reach 0.1Hz. The system exhibits low measurement error and good stability, indicating a promising application prospect in carbon dioxide concentration detection based on QCM.