ZnAl2O4 is a cubic close‐packed oxide with tetrahedral and octahedral sites in the lattice structure. The catalytic activity of ZnAl2O4 is strongly connected with the surface properties caused by the partially inverse spinel ZnAl2O4 structure. In this research, ZnAl2O4 catalysts are prepared for the glycerolysis of urea via the polymeric citrate complex method using polymeric templates made of citric acid with a different polyol precursor. Depending on the polyol precursor, the partial inversion parameters representing the disordered bulk ZnAl2O4 structure are controlled, which results in different surface AlO4/AlO6 ratios and surface acidity. The specific surface areas of the prepared ZnAl2O4 catalysts are proportional to the molecular weight of the polyol precursor. The s–ZnAl2O4 (polyol precursor = sorbitol) prepared via two pathways from citrate complex and polymeric citrate complex shows the highest inversion parameter and surface acidity, leading to the highest glycerol carbonate (GC) yield and glycerol conversion in the glycerolysis of urea. A relationship between the GC yield and the surface properties, such as the acidity and inversion parameters, is established.