Nitrogen oxides (NOx), pivotal atmospheric pollutants, significantly threaten the environment and human health. The CH4-SCR process, leveraging the abundance and accessibility have methane, 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 H2O, 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, which was synthesized via ion exchange and meticulously optimized for preparation conditions, including calcination temperature and In ions concentration, and reaction conditions, including CH4/NO ratio, O2 concentration, H2O content, and Gas Hourly Space Velocity (GHSV). Furthermore, long-term operation tests and stability tests were conducted on the In/H-SSZ-39 catalyst. In addition, a series of characterizations were conducted to delve into the reasons behind how preparation conditions influence catalytic activity, as well as to investigate the changes in physicochemical properties during the reaction process.