The carriers for hydrophobic bioactives have been extensively studied, while those for hydrophilic bioactives are still challenging. The partition of bioactives in the particles depends greatly on their solubility, interaction with carrier materials, as well as structure of carriers. In this study, chitosan-coated hollow zein particles using calcium phosphate as a sacrificing template (CS-HZ) were fabricated to co-encapsulate folic acid (FA) and caffeic acid (CA). Partition, photostability, and antioxidant capacity of bioactive compounds were also studied. The size, polydispersity index and ζ-potential of optimized CS-HZ were 176.3 nm, 0.14 and +39.3 mV, respectively, indicating their small and uniform dimension with excellent colloidal stability. FA interacted with chitosan to form complexes and then coated on the zein particles where CA was encapsulated. After co-encapsulation in CS-HZ, the photostability of both FA and CA was improved in comparison with encapsulation of single compound, with 85% of FA remaining after 240 min of UVA irradiation, and 90% of CA remaining after 80 min. Antioxidant activity of CA decreased upon encapsulation, but significantly increased after irradiation. Findings in this study shed some light on the design of carriers for co-delivery of hydrophilic compounds in acidic condition.