Nitrogen oxides (NOx), pivotal atmospheric pollutants, significantly imperil the environment and human health. The CH4-SCR process, leveraging the abundant and accessible methane (CH4), emerges as a promising avenue for NOx abatement. Previous studies have demonstrated that zeolite support with twelve-membered ring (12-MR) and five-membered ring (5-MR) structures are susceptible to framework collapse in the presence of water, leading to catalyst deactivation. Consequently, there is a necessity to explore novel zeolites with enhanced hydrothermal stability for application in CH4-SCR processes. This research introduced for the first time an investigation into a novel In-H-SSZ-39 catalyst, synthesized via ion exchange and meticulously optimized for preparation conditions, including calcination temperature, In ions concentraiton, and reaction conditions, including CH4/NO ratio, O2 concentration, water vapor content, and Gas hourly space velocity (GHSV). Notably, the In/H-SSZ-39 catalyst achieved superior performance of 42.1% at 605 °C, with a calcination temperature of 500 °C and an In ion concentration of 0.066 M, under CH4/NO ratio of 1.5:1, 10% O2, and GHSV of 21000 h-1. In addition, the catalytic performance was influenced by the concentration of water vapor and the GHSV value.