• A magnetically reusable acid microsphere was developed for biodiesel synthesis. • 97.8 % biodiesel yield was obtained from fatty acids and non-food oils at 65 °C. • Acid catalyst provided proton to promote esterification as revealed by DFT. • The acid microsphere was recycled with constant activity in 5 consecutive times. • Satisfactory activity and generality in biodiesel synthesis with various feedstocks. Biodiesel, a kind of promising alternative renewable energy, is of great significance in replacing conventional fossil energy resources. Herein, for purpose of improving the preparation technology of biodiesel through efficient and convenient modifying the well-dispersion of active sites of magnetic catalysts, Fe 3 O 4 @SiO 2 -SO 3 H (P) and Fe 3 O 4 @SiO 2 -SO 3 H (S) catalysts synthesized respectively via co-precipitation and solvothermal preparation methods, were successfully employed for biodiesel production. Fe 3 O 4 @SiO 2 -SO 3 H (S) bearing the uniform core-shell nanometer microsphere structure and good dispersibility that was beneficial to the substrates touch with efficient acidic sites along with acid density of 1.8 mmol g −1 , was demonstrated to furnish biodiesel in a higher yield of 97.8 %, which was better than that of Fe 3 O 4 @SiO 2 -SO 3 H (P) (88.2 % yield) at 65 °C within 4 h. The kinetic study revealed that Fe 3 O 4 @SiO 2 -SO 3 H (S)-catalyzed esterification fitted the first order model along with a low activation energy (47.9 kJ/mol), further clarifying the reason for the good catalytic performance of Fe 3 O 4 @SiO 2 -SO 3 H (S). More importantly, thermal filtration and reusability experiments confirmed the catalyst heterogeneous catalytic behavior and good reusability. The involved reaction mechanism was also interpreted, in which the Fe 3 O 4 @SiO 2 -SO 3 H (S) acid catalyst was determined to be favorable for accelerating oleic acid conversion to biodiesel via density functional theory (DFT) calculations. Finally, given economic and environmental perspective, by analyzing the potential of the industrial application of Fe 3 O 4 @SiO 2 -SO 3 H (S) and comparing its catalytic performance with other reported catalysts, its promising value in terms of transforming fatty acids and non-food oils into biodiesel could be anticipated.