Compressed natural gas (CNG) taxis represent the most ubiquitous and dynamically active passenger vehicles in urban settings. The pollutant emission characteristics of in-use CNG taxis driving on a typical mountain city before and after three-way catalyst (TWC) replacement was examined using a modular on-board portable emissions measurement system (PEMS), the OBS-ONE developed by Horiba. The results showed that the exhaust NO of CNG taxis equipped with deactivation TWC exceeded the emission limits, even higher than gasoline vehicles. The high emission rate of CNG taxis is mainly concentrated on road slopes between a 2% and 6% gradient and a deceleration rate in the interval of [0.5, 4], respectively, which results in higher emissions from CNG taxis traveling in the mountain city of Chongqing than other cities and vehicles. Moreover, the pollutant emission rates of the in-use CNG taxis were highly correlated with the velocity and the vehicle specific power (VSP). After a new TWC replacement, the emission factors of carbon monoxide (CO), total hydrocarbons (THC), nitrogen oxides (NOx), and particle number (PN) decreased by 85.21–89.11%, 68.71–85.49%, 60.91–81.11%, and 62.26–68.39%, respectively. Our results will provide guidance for urban environments to carry out the comprehensive management of in-use vehicles and emphasize the importance of TWC replacement for CNG taxis.