Rutin is a natural compound that is widely distributed in various plants. Increasing lines of evidence have proved that rutin has a beneficial effect on cardiovascular health, oxidative stress, and blood glucose control. However, the application of rutin is limited due to its poor solubility and low oral bioavailability. To improve the bioavailability of rutin, two cocrystals of rutin with L-proline and D-proline were prepared successfully, and multiple characterization methods were utilized to study the physicochemical properties of rutin and its cocrystals. The powder dissolution in vitro and the pharmacokinetic behavior in vivo were also evaluated. The results indicated that Rut-L-Pro exhibited a significantly improved solubility, and the oral bioavailability also had great improvement; the AUC 0−10h of Rut-L-Pro was 5.6-fold that of rutin, and C max was 3.8 times. As a result of the improvement of rutin bioavailability, Rut-L-Pro performed better blood glucose control and cardioprotective activities.