The objective of this work is to design and fabricate a natural zein-based nanocomposite with core-shell structure for the delivery of anticancer drugs. As for the design, folate-conjugated zein (Fa-zein) was synthesized as the inner hydrophobic core; soy lecithin (SL) and carboxymethyl chitosan (CMC) were selected as coating components to form an outer shell. As for fabrication, a novel and appropriate atomizing/antisolvent precipitation process was established. The results indicated that Fa-zein/SL/CMC core-shell nanoparticles (FZLC NPs) were successfully produced at a suitable mass ratio of Fa-zein/SL/CMC (100:30:10) and the freeze-dried FZLC powder showed a perfect redispersibility and stability in water. After that, docetaxel (DTX) as a model drug was encapsulated into FZLC NPs at different mass ratios of DTX to FZLC (). When = 1:15, DTX/FZLC NPs were obtained with high encapsulation efficiency (79.22 ± 0.37%), small particle size (206.9 ± 48.73 nm), and high zeta potential (-41.8 ± 3.97 mV). DTX was dispersed in the inner core of the FZLC matrix in an amorphous state. The results proved that DTX/FZLC NPs could increase the DTX dissolution, sustain the DTX release, and enhance the DTX cytotoxicity significantly. The present study provides insight into the formation of zein-based complex nanocarriers for the delivery of anticancer drugs.