Dissolved gases are key byproducts of biogeochemical reactions and serve as critical indicators for the evolution of aquatic ecosystems. However, traditional headspace equilibrium sampling methods are prone to air contamination, decompression-induced degassing, and limited measurement precision. To address these challenges, this study developed an in-situ system for the simultaneous determination of multiple dissolved gases in deep waters. The method was applied to characterize the distribution of dissolved gases in the Three Gorges Reservoir. Results demonstrated that the proposed method achieves high-precision, simultaneous in-situ measurements of five key gases—methane (CH4), nitrogen (N2), oxygen (O2), argon (Ar), and carbon dioxide (CO2)—at depths of up to 100 meters. High-precision calibration models were established for these five gases through systematic multi-temperature and multi-concentration calibration, achieving a measurement resolution of 1 ppm. Compared to traditional headspace sampling, this approach effectively eliminates air interference and decompression degassing, significantly enhancing data fidelity. Field validation against commercial high-precision instruments (Picarro greenhouse gas analyzer and multi-parameter water quality sondes) demonstrated exceptional consistency (R2 > 0.96; Concordance Correlation Coefficient [CCC] > 0.98), confirming the accuracy and reliability of the measurements. Furthermore, the proposed method surpasses traditional techniques in terms of real-time performance, spatial resolution, and monitoring efficiency. Field application in the Pengxi River Bay of the Three Gorges Reservoir successfully generated high-resolution two-dimensional distribution profiles along a 42-km longitudinal section. The results clearly revealed distinct vertical stratification, extensive bottom water hypoxia, and coupled accumulation of CO2 and CH4 during summer and autumn, effectively identifying hotspots of intense biogeochemical activity. This in-situ monitoring technology matches the accuracy of traditional laboratory methods while offering superior data fidelity, spatiotemporal resolution, and monitoring efficiency. It provides innovative technical support for greenhouse gas emission assessment, water quality management, aquatic nitrogen cycling, and the study of material cycling and ecological evolution in complex aquatic environments.