The invention provides an integrated process and system for detecting and treating toxic gas in deep natural gas. The process comprises the steps; drying deep natural gas after cooling and depressurizing; sequentially carrying out radon, hydrogen sulfide and mercury detection on the dried deep natural gas; if the concentration of mercury, radon and hydrogen sulfide in the deep natural gas reaches the standard after detection, conveying the deep natural gas to a gas conveying pipeline; if it is found that the concentration of radon, hydrogen sulfide and mercury in the deep natural gas does not reach the standard after detection, carrying out harmless treatment on radon, part of mercury, hydrogen sulfide and the rest of mercury in the deep natural gas in sequence; carrying out mercury, radon and hydrogen sulfide detection on the deep natural gas subjected to harmless treatment in sequence, and if the concentrations of mercury, radon and hydrogen sulfide in the deep natural gas reach the standard, conveying the deep natural gas subjected to harmless treatment to a gas conveying pipeline; and if the concentrations of mercury, radon and hydrogen sulfide in the deep natural gas do not reach the standard, carrying out harmless treatment on the radon, part of mercury, hydrogen sulfide and the rest of mercury in the deep natural gas in sequence until reaching the standard.