In this work, a type of natural microspheric soil conditioner, PZ(Fe)/GL-SA-Urea, was prepared by emulsion cross-linking and sharp-hole coagulation bath methods. Gelatin (GL) and sodium alginate (SA) were selected as the outermost shell, and the prepared FeOOH was loaded on pickling zeolite (PZ) to improve the loading ratio of urea. The embedding performance and sustained release behavior of the microspheres showed that when the concentration of urea was 1.5%, the embedding rate reached 37.63%, and the cumulative release rate reached 68% within 100 h, indicating that the microsphere had good encapsulation and sustained release abilities. In addition, the water retention and swelling behaviors of the microspheres can be obtained by controlling the content of added GL. Furthermore, antibacterial and planting experiments revealed that the microspheres had excellent antibacterial effects and can effectively improve soil quality and promote crop growth. Therefore, the PZ(Fe)/GL-SA-Urea microsphere soil conditioners possess good application properties and provide fresh solutions to improve soil quality and raise crop yields.