Rivers are important ecosystems for carbon emissions and play a crucial role in the global carbon cycle. However, CO2 and CH4 emissions from subtropical rivers are substantially under‐represented in global‐scale estimates. Here, we explored the regional patterns of riverine CO2 and CH4 dynamics in the Pearl River basin with a subtropical monsoon climate. We found that its CO2 and diffusive CH4 emissions showed a decreasing trend with increasing stream order. Seasonality in CO2 and diffusive CH4 emissions was primarily driven by variations in partial pressure of CO2 (pCO2) and CH4 (pCH4) and gas transfer velocities, which were strongly regulated by hydrology and climate. We further estimated the basin‐wide CO2 and diffusive CH4 fluxes at 17.8 ± 7.4 Tg C yr−1 and 191.5 ± 139.9 Gg C yr−1, respectively. When normalized to the water surface, the mean diffusive fluxes were 790.1 and 8.5 mmol m−2 d−1 for CO2 and CH4, respectively, which were 1.3 and 2.5 times higher than the global mean riverine CO2 and CH4 fluxes, respectively. This suggests that the global significance of subtropical rivers is probably underestimated because their substantially higher CH4 fluxes are unaccounted for. Furthermore, compared with measured pCO2, the alkalinity‐based pCO2 could introduce significant errors by 20% at ∼30% of the sampling sites, underscoring the necessity of direct measurements to reduce uncertainty. This study provides the first estimate of basin‐wide CO2 and diffusive CH4 emissions in the PRB through direct pCO2 and pCH4 measurements, and highlights the role of hydrologic and climatic factors in governing riverine carbon emissions.