We developed a new class of acid-base bifunctional heterogeneous catalyst, which can be used in the transesterification of rapeseed oil for highly efficient biodiesel production. A simple Keggin-type HPA (heteropoly acid) functionalization on the surface of zeolitic imidazolate framework-8 (ZIF-8) nanoparticles, through an imidazolium medium, results in the bifunctional heterogeneous catalysts. The hybrid materials exhibit a novel hierarchically core-shell nanostructure, which provides a large surface area and interconnectivity, leading to a thin wrinkled HPA shell at the surface of rhombic dodecahedral ZIF-8 core crystals. A strong O-N hybrid bonding through an electrostatic effect in the hybrid materials demonstrates a strong interaction between the Keggin and imidazole units, which is one of the main driving forces of hybrid materials formation. Additionally, the transformation of the HPA/ZIF-8 ratio in the hybrid materials changes the acidity and basicity, thereby affecting catalyst activity. We used these bifunctional core-shell materials as environmentally friendly heterogeneous catalysts in the transesterification of rapeseed oil with methanol to produce a high-quality biodiesel. Of particular interest, the HPA-functionalized ZIF-8 catalyst with a proper HPA/ZIF-8 ratio shows a high FAME conversion of 98.02% along with high recyclability because of the sufficiently large surface area and bi-functionality of strong acidity. Furthermore, the HPA-functionalized ZIF-8 catalyst shows a high reaction efficiency of the benzyl alcohol oxidation process, indicating a great potential of our catalyst to a wide range of applications.