Multifunctional magnetic polydopamine (PDA) nanospheres have become a research hotspot, especially in the field of biocatalysis, owing to their good biocompatibility and abundant functional groups. However, facile and rapid synthesis of hollow magnetic mesoporous PDA (HM-MPDA) with high saturation magnetization, large tailored pore size, excellent structural thermal stability, and controllable shell thickness is still a challenge. Herein, HM-MPDA nanospheres with ultrahigh magnetization (∼82.2 emu/g), ultra-large tunable pore sizes (11.53−49.53 nm), rigid pore structures (at 550 °C), and controllable shell thickness (23−178 nm) are synthesized based on a novel nanoemulsion co-assembly approach. Impressively, the hollow magnetic mesoporous PDA nanoflowers (HM-MPDA-NFs) are obtained by simply adjusting the amount of 1,3,5-trimethylbenzene and the P123/ F127 weight ratios. Considering their unique properties, lipases were successfully immobilized on the pore walls of HM-MPDA-NFs, which were employed for the preparation of biodiesel. Under the optimum esterification conditions, the conversion of biodiesel can reach up to 87.9% and still exceed 71.3% after six times of recycling. More importantly, this study opens up a new way to fabricate hollow magnetic mesoporous nanocarriers, which can provide many applications in biocatalysis, dye adsorption, electrochemistry, and biosensing.