In many regions, even if waste vegetable oil is used as raw material, the profits of biodiesel (fatty acid methyl ester, FAME) enterprises still remain restricted, and they are facing environmental problems caused by the by‐product glycerol. Hence, value‐added utilization of FAME and glycerol is a promising alternative to improve the competitiveness of biodiesel enterprises in the economy and environmental protection. In this paper, FAME and glycerol were utilized to prepare epoxidized acyl glycerides by transesterification and epoxidation. In the transesterification, acyl glycerides were prepared by reacting FAME and glycerol catalyzed by K2CO3. The contents of monoacyl glyceride, diacyl glyceride, and triacyl glyceride in the acyl glycerides were about 50%, 40%, and 10%, and the optimal conditions were a temperature of 200°C and the molar ratio of FAME to glycerol of 1:1. In the epoxidation, selectivity of epoxides was significantly affected by monoacyl glyceride content, and a treatment method was developed to control the monoacyl glyceride content <5%. In addition, the plasticity of epoxidized acyl glycerides to partially substitute dioctyl phthalate in polyvinyl chloride was studied, the overall mechanical properties, thermal stability, and extraction resistance were improved. In this work, FAME and glycerol were utilized to prepare epoxidized acyl glycerides with higher value‐added, which provide a potential solution for improving the market competitiveness of biodiesel enterprises.