Orbitrap mass spectrometers have gained widespread popularity in ground-based environmental component analysis. However, their application in atmospheric exploration for space missions remains limited. Existing data acquisition solutions for Orbitrap instruments primarily rely on commercial systems and computer-based spectrum analysis. In this study, we developed a self-designed data acquisition solution specifically tailored for atmospheric molecule detection. The implementation involved directly integrating a spectrum analysis algorithm onto a field programmable gate array (FPGA), enabling miniaturization, real-time performance, and meeting the desired requirements. The system comprises signal conditioning circuits, analog-to-digital conversion (ADC) circuits, programmable logic circuits, and related software. These components facilitate real-time spectrum analysis and signal processing on hardware, enabling high-speed acquisition and analysis of signals generated by the Orbitrap. Experimental results demonstrate that the system can sample front-end analog signals at a rate of 25 MHz and differentiate signal spectra with an error margin of less than 7 kHz. This establishes the viability of the designed data acquisition system for atmospheric mass spectrometry analysis.