Nitrogen oxides (NOx) have become a critical environmental concern, necessitating the development of highly efficient catalysts for temperature which is lower than 300 °C. Selective catalytic reduction with NH3 (NH3-SCR) is a process where ammonia is the reducing agent for selective catalytic reduction of nitrogen oxides in exhaust gases. The mechanism-property relationship between catalytic active sites and low-temperature denitrification efficiency, however, remains unclear. In this study, we synthesized a series of cobalt-modified nanoparticle catalysts using a scalable citric acid sol-gel method and conducted comprehensive characterizations. Our findings indicate that an optimal cobalt doping rate significantly enhances catalytic activity due to the synergistic effects of reduced nanoparticle size and the dual active sites of Co0/Co2+. Specifically, at a cobalt doping ratio of 1.0, the catalyst demonstrates peak SCR activity, achieving 85.5% NOₓ conversion at 120 °C and complete conversion at 150 °C. These cobalt-modified nanoparticle catalysts feature high deposition of doped Co ions on their surfaces, predominantly as metallic cobalt and CoOx nanoclusters. Compared to undoped samples, the cobalt-doped nanoparticle catalysts exhibit a greater specific surface area, increased acidity, enhanced chemisorbed oxygen, and improved redox properties, all contributing to superior denitrification efficacy. Additionally, Density Functional Theory (DFT) calculations provide assertive evidence into the reaction mechanism, showing that Co2+ sites effectively adsorb and activate NH₃, while Co0 sites are crucial for NO adsorption and activation. The synergistic interaction between Co2+ and Co0 facilitates NN coupling, enhancing overall reaction efficiency. These findings underscore the potential of cobalt-modified catalysts for practical industrial applications, offering robust performance over a wide temperature range and meeting stringent environmental regulations.