Lime application is known to effectively increase rice yield and mitigate soil acidification, but its effect on the leaching losses of carbon (C) and nitrogen (N) from paddies remain unclear. Here, two treatments (no liming as control and liming at a rate of 2.0 t ha as (Ca(OH))) were conducted in a double-cropped rice field with acidic red soil. The results indicated that liming significantly increased grain yield by 12.7% and 12.3% in the early and late rice season relative to the unlimed treatment, respectively. The concentration of ammonium N (NH-N) in leachates was low and no significant difference was observed between the two treatments. Liming significantly increased the leaching losses of nitrate N (NO-N, + 29.6%) at the mid-tillering stage and dissolved organic N (DON, + 48.9%) at the seedling stage in the early rice season relative to the unlimed control. In the late rice season, liming raised the leaching losses of NO-N by 14.1% at the seedling stage, but had no significant effect on DON. In addition, liming significantly increased the leaching losses of dissolved organic C (DOC) except at the grain filling of early rice. Liming did not affect the leaching losses of DOC in the late rice season. In conclusion, liming improves grain yield but promotes the risk of the leaching losses of dissolved C and N in the double cropped-rice system. While applying lime to ameliorate soil acidification, we suggest that appropriate practices should be employed to reduce C and N leaching to protect groundwater quality.