Abstract: Ensemble prediction has been an important tool for weather forecasting, sub-seasonal to seasonal prediction, seasonal prediction, interannual prediction and even simulation of climate change, which has garnered widespread attention in the field of meteorology. This paper introduces the ensemble prediction scheme of China Meteorological Administration Climate Prediction System Version 3 (CMA-CPSv3). In this scheme, we adopt the approach of combining stochastic perturbations of physical process tendencies in the atmosphere, the air-sea flux and time-lagged initial values. Based upon the Version 2 of High-Resolution Beijing Climate Centre Climate System Model (BCC-CSM2-HR), we have developed a multi-layer random perturbation ensemble prediction system with relatively good ensemble sample dispersion, stability, and reliability. Results of evaluation for hindcasts over the past 20 years show that this ensemble prediction system significantly improves the prediction of precipitation and 2 m temperature over China, as well as the El Niño-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD) and Asian Monsoon. In particular, the random perturbation of air-sea flux shows a positive effect on improving the prediction skills of ENSO and Southeast Asian Monsoon (SEAM) and Western North Pacific Summer Monsoon (WNPSM) indices. This study offers useful insights for further characterizing uncertainty in other component models of the climate system.