The study investigates the combination of microfiltration (MF) with traditional thermal pasteurization (TP), high-pressure processing (HPP), and electron beam irradiation (EBI) in the production of cloudy apple juice. Using 0.22 μm MF membranes instead of 0.45 or 0.1 μm, the highest flux was achieved, the permeate and retentate exhibited minimal deviation from raw apple juice (RAJ) in terms of physicochemical indicators. MF divided RAJ into a cloudy retentate containing microorganisms and a clarified permeate in a 1:4 vol ratio. The retentate was then pasteurized by HPP, TP, and EBI, after which it was mixed with the permeate to create cloudy apple juice. This innovative process reduced processed juice volume by 80% compared to single pasteurization method, decreased the loss of volatile compounds by 20.05%–33.52%, and cut energy consumption by 72.29%–75.35%. Overall, the hybrid pasteurization strategy approach shows great promise pasteurization technique for producing high-quality cloudy apple juice.