Japanese cypress (Chamaecyparis obtusa) is a recalcitrance softwood widely used as building material in Japan. A combined technique of alcohol-based organosolv treatment and ball milling (BM) of this softwood for the production of fermentable sugars from lignocellulose was investigated. Ethanol, ethylene glycol, water, and their mixtures were used as solvents, and acetic acid was used as a proton donor. After solvolysis, a residual sample was subjected to short-time BM, and the entire residue was evaluated by saccharification with Acremonium cellulase. Short-time BM after alcohol-based organosolv treatment greatly improved the enzymatic digestibility and decreased the required severity of organosolv treatment. Moreover, alcohol-based organosolv treatment increased the efficiency and reduced the time required for BM despite small quantity of removed lignin. It was found that the combination of alcohol-based organosolv treatment in mild condition and short-time BM had a synergistic effect on the enzymatic digestibility of Japanese cypress.