To improve the water solubility and dissolution rate, genipin was nanocrystallized by an emulsion solvent evaporation method, followed by freeze‐drying. The optimization condition of nanocrystallization process was carried out by single‐factor experiment. The effects of five experimental parameters, such as concentration of surfactants the proportion of water to organic phase, homogenate speed and time, homogenization pressure and times, and the proportion of genipin to lyoprotectants on the mean particle size (MPS) of genipin nanoparticles, were investigated. Under the optimum conditions by single‐factor experiments, genipin nanoparticles with an MPS of 59.8 nm were obtained. The genipin nanoparticles were characterized by SEM, FTIR, XRD, DSC, solvent residue, drug purity test, dissolution testing, and bioavailability analysis. The analysis results indicated that the chemical structure of genipin nanoparticles was unchanged, but the crystallinity was reduced. The solubility of genipin nanoparticles was 9.05 times of the raw drug. In addition, the residual amounts of chloroform and ethanol were separately less than the ICH limit for class II, and the oral bioavailability of the genipin nanoparticles powder was 7.99 times of raw genipin. According to the results above, genipin nanoparticles show the potential application value of its oral absorption.