This study developed a novel approach that integrated climate model selection and multi-model ensemble (MME) construction to effectively represent model uncertainties and, consequently, improve consistency in the evaluation of changes to extreme rainfall in different scenarios. Our focus was to combine 10 regional climate model (RCM) simulations, forced by two global climate models (GCM), especially for estimation of design rainfall in a changing climate. We hypothesized that the natural variability and statistically higher moment attributes in the extreme rainfall simulations from RCMs were not fully preserved. Therefore, the MME approach could be more effective in climate change studies, largely due to the use of multiple climate models. First, an experimental study was proposed to validate the efficacy of the proposed modeling framework approach adopting L-moments to quantify relative importance among climate models and their use for representing natural variability in the MME construction. The proposed approach was then applied to climate change scenarios collected from multiple RCMs for the Han-River watershed during both historical (1981–2005) and future (2006–2 100) periods. The results showed that the climate model selection informed by natural variability demonstrated better performance, representing nearly identical distribution to the observed annual maximum rainfall (AMR) in the Han River watershed. The range of the selected scenario was relatively narrower than that of all the scenarios, and the change rate was more consistent with the limited zero crossing, reflecting improvement in both model performance and consistency over historical and future periods, respectively. The change rate of the MME under RCP8.5 appeared to be an approximately 20% increase for the near (2011–2040) and far (2071–2 100) future, and the degree of increase in the rate for the mid-future (2041–2070) was slightly lower than that for the other periods, with increase of approximately 10%.