In this study, Genipin as a novel crosslinking agent was used to prepare the crosslinked Bacillus subtilis alkaline protease aggregates (BAP-CLEAs). Using the recovery rate of enzyme activity as the main indicator, the optimal processing conditions for the preparation of BAP-CLEAs were determined: mass concentration of the crosslinking agent 0.50%, crosslinking temperature 35 ℃ and crosslinking time 12 h. The recovery rate of the enzyme activity of the BAP-CLEAs prepared under the optimum condition was 55.04%. The characterization results of the BAP-CLEAs by SEM and FTIR showed that Bacillus subtilis alkaline protease was successfully crosslinked with the aid of genipin. Compared with the free enzyme, the optimal pH of BAP-CLEAs shifted towards the alkaline direction (from 9.4 to 10.3), and a relatively high enzyme activity was maintained in wide pH and temperature ranges. In addition, BAP-CLEAs still had 86.42% of the initial enzyme activity after 5 repeated uses in a casein substrate at 2%. The above catalytic characteristics indicated that the Bacillus subtilis alkaline protease could be successfully crosslinked to form CLEAs with the aid of genipin. The BAP-CLEAs had superior pH stability, temperature stability and repeatability compared with the free enzyme, thus has a good industrial application prospect.