This study investigated the effects of activating convective parameterization (CP) in higher-resolution domains of a regional climate model, the Weather and Research Forecast (WRF) model, on watershed-scale precipitation by means of sensitivity analysis. The sensitivity analysis was conducted over three watersheds in the Hokkaido region, Japan. Three nested domains of 27, 9, and 3 km of horizontal resolution were set over the three study watersheds. Then, two types of sensitivity analysis were conducted. First, 36 of the single-year simulations were run with 12 combinations of two cloud microphysics (MP) schemes and six CP schemes and with three types of CP activation; activating a CP scheme only in the outermost domain, in the outermost and middle domain, and in all three domains. After the single-year simulations, long-term (32-year) simulations were conducted using an MP × CP combination with the three types of CP activation. The two-sensitivity analysis shows that activating CP in the higher-resolution domains does not always improve watershed-scale precipitation, but it has a high possibility of improving the results. Moreover, the improvement via activating CP in higher-resolution domains may continue for a long-term period.