The invention discloses a swelling-type hollow silk fibroin micro-needle drug delivery system and a preparation method thereof. According to the technical scheme of the preparation method, a swelling modified silk fibroin solution is casted in a PDMS mold to be vacuumized, dried and molded as a hollow needle-type housing. After that, a silk fibroin micro-needle array provided with cavities in the hollow needle-type housing is filled with powder-like or solution-like drugs, vacuumizing and drying are carried out to form a drug part. Finally, a layer of modified silk fibroin solution is cast, dried and molded as a cladded coating. The cladded coating is removed to obtain the swelling-type hollow silk fibroin micro-needle drug delivery system. The drugs are wrapped inside the cavities of the silk fibroin micro-needle arrays, so that the system is high in drug loading ratio and low in skin allergenicity and stimulation. The system facilitates the sustained release and the controlled release of micro-needle drugs. Meanwhile, according to the preparation method, since the swelling modified silk fibroin solution is cast, dried and molded in a mild processing condition, the system is low in processing cost and suitable for large-scale production. Drugs are directly wrapped in the cavities of the swelling hollow micro-needles, so that controlled-release drugs are swelled in the micro-needle base material. In this way, the biological activities of the controlled-release drugs are maintained, while the structure of the hollow silk fibroin micro-needle drug delivery system is greatly simplified. The system is better in practicality.