Pickering emulsions (PEs) have been regarded as an effective approach to sustaining and preserving the bioactivities of essential oils. The aim of this research is to prepare a PE stabilized by chitosan/alginate nanoparticles (CS-SA NPs) for the encapsulation and stabilization of D-limonene. In this work, the influence of calcium ions (Ca) on the morphology and interaction of nanoparticles was studied, and then the preparation technology of CS-SA/Ca NPs was optimized. The results showed that the presence of Ca reduced the size of the nanoparticles and made them assume a spherical structure. In addition, under the conditions of 0.2 mg/mL CaCl, 0.6 mg/mL SA, and 0.4 mg/mL CS, the CS-SA/Ca NPs had the smallest size (274 ± 2.51 nm) and high stability (-49 ± 0.69 mV). Secondly, the PE was prepared by emulsifying D-limonene with CS-SA/Ca NPs, and the NP concentrations and homogenization speeds were optimized. The results showed that the small droplet size PE could be prepared with 2 mg/mL NP and a homogenization speed of 20,000 r/min, and it had excellent antibacterial and antioxidant activities. Most importantly, the emulsion showed higher activity, higher resistance to ultraviolet (UV) and a higher temperature than free D-limonene. This research provides a feasible solution for the encapsulation, protection and delivery of essential oils.