Wine lees is a low value biomass resource rich in cellulose, with great potential for producing organic fertilizers and chemicals. However, the high acidity of wine lees limits the catalytic efficiency of the conversion tool endoglucanase. Here, we expressed endoglucanase tCel5A from Trichoderma reesei in Pichia pastoris, and the combination of promoter AOX1 and signal peptide SUC2 resulted in a highly active expression of 4632.81 U/mg. Subsequently, the catalytic center design and surface charge modification strategy resulted in mutants T88H/W255H and S45D/T55D/T59D exhibiting catalytic activity twice and three times higher than WT at pH 3.0, respectively. Finally, when the solid-liquid ratio was 1:15 (w/v), the degradation rate of wine lees was nearly double that of WT. The degradation products contained a variety of industrial and pharmaceutical raw components, including the antioxidant and anticonvulsant isopiperolein B. This study accelerates the green and sustainable management of wine lees.