This study aimed to protect phenolic compounds of Cyclocarya paliurus (Batal.) Iljinskaja (C. paliurus) using a microencapsulation technique. Ethanol and aqueous extracts were prepared from C. paliurus leaves and microencapsulated via microfluidic-jet spray drying using three types of wall material: (1) maltodextrin (MD; 10–13, DE) alone; (2) MD:gum acacia (GA) of 1:1 ratio; (3) MD:GA of 1:3 ratio. The powders’ physicochemical properties, microstructure, and phenolic profiles were investigated, emphasizing the retentions of the total and individual phenolic compounds and their antioxidant capacities (AOC) after spray drying. Results showed that all powders had good physical properties, including high solubilities (88.81 to 99.12%), low moisture contents (4.09 to 6.64%) and low water activities (0.11 to 0.19). The extract type used for encapsulation was significantly (p < 0.05) influenced the powder color, and more importantly the retention of total phenolic compounds (TPC) and AOC. Overall, the ethanol extract powders showed higher TPC and AOC values (50.93–63.94 mg gallic acid equivalents/g and 444.63–513.49 µM TE/g, respectively), while powders derived from the aqueous extract exhibited superior solubility, attractive color, and good retention of individual phenolic compounds after spray drying. The high-quality powders obtained in the current study will bring opportunities for use in functional food products with potential health benefits.