Pemafibrate is a new generation of anti-hyperlipidemia drugs. However, its poor solubility in water (0.410 mg/mL at 25 °C) has limited its oral bioavailability. In this study, we aimed to improve the solubility and consequently the oral bioavailability of pemafibrate via a new polymorph. A new polymorph Form II was successfully obtained by controlling the crystallization temperature and characterized by multiple analysis methods. The thermodynamic properties of Form I and Form II are almost the same, the melting points of crystal Form I [differential scanning calorimetry (DSC) onset: 97.5 °C, melting entropy: -76 J/g] and crystal Form II (DSC onset: 96.6 °C, melting entropy: -80 J/g) are very close, and the crystallinity of both is very high. In pure water, Form II is about 1.9 times that of Form I in terms of the intrinsic dissolution rate (IDR) and powder solubility. In medium, the IDR characterization was performed in a pH 6.8 buffer. The solubility of this Form II in 0.1 M HCl (pH 1.0) and phosphate buffers (pH 6.8) was investigated, and the results showed that the solubility of Form II was 2.1 and 2.0 times that of Form I, respectively. The crystal structure of Form II shows that the hydrophilic carboxyl groups of the compound are arranged outside the unit cell, which may be the reason for the increased solubility. We also studied the pharmacokinetics of beagle dogs. The mean AUC0-24h of Form II is about 2.6 times that of Form I, indicating that the solubility and bioavailability of pemafibrate can indeed be improved by forming the new polymorph Form II. It may become an ideal solid form of active pharmaceutically ingredient suitable for pharmaceutical preparations, and it can be further studied in the later period.