Deep understanding of the effects of precipitation on carbon budgets is essential to assess the carbon balance accurately and can help predict potential variation within the global change context. Therefore, we addressed this issue by analyzing twelve years (2003-2014) of observations of carbon fluxes and their corresponding temperature and precipitation data in a subtropical coniferous plantation at the Qianyanzhou (QYZ) site, southern China. During the observation years, this coniferous ecosystem experienced four cold springs whose effects on the carbon budgets were relatively clear based on previous studies. To unravel the effects of temperature and precipitation, the effects of autumn precipitation were examined by grouping the data into two pools based on whether the years experienced cold springs. The results indicated that precipitation in autumn can accelerate the gross primary productivity (GPP) of the following year. Meanwhile, divergent effects of precipitation on ecosystem respiration (Re) were found. Autumn precipitation was found to enhance Re in normal years but the same regulation was not found in the cold-spring years. These results suggested that for long-term predictions of carbon balance in global climate change projections, the effects of precipitation must be considered to better constrain the uncertainties associated with the estimation.