Melatonin (MLT) is a small molecule with low water solubility and high permeability. According to the Biopharmaceutics Classification System, MLT is a class II drug exhibiting a very short half-life and minimal and variable bioavailability. This work aimed to establish a delivery system composed of an enteric MLT nanosphere with favorably controlled and sustained release characteristics superior to those of raw MLT. The nanosphere was composed of hydroxypropyl methylcellulose phthalate (HP55) and silica (SiO2) with MLT. As a carrier, SiO2 contains numerous surface pores with high adsorption capacity advantageous for permeability and slow release. HP55 is a good enteric coating material. MLT-loaded SiO2 was obtained through adsorption in acetone solution. A MLT-loaded SiO2 coated with HP55 (MLT-SiO2-HP55) nanosphere was prepared via desolvation. The characteristics of this nanosphere were analyzed through transmission electron microscopy, Brunauer–Emmett–Teller surface area analysis, diffuse reflectance infrared Fourier transform spectroscopy, X-ray diffraction, differential scanning calorimetry, and thermogravimetric analysis. Results show that MLT was loaded mostly in the pores of SiO2. HP55 was coated on a large portion of MLT-SiO2. In vitro release studies revealed that the release rate of MLT from MLT-SiO2 was higher than that of raw MLT in simulated gastric fluid (SGF). The amount of MLT released from MLT-SiO2-HP55 in SGF was lower than that released from simulated intestinal fluid because of HP55 coated on MLT-SiO2. In vivo evaluation demonstrated the controlled drug release of MLT-SiO2-HP55 in rats. Compared with raw MLT, MLT-SiO2-HP55 prolonged peak time (Tmax) from 15 min to 30 min and increased peak concentration (Cmax) from 168.86 ng/mL to 383.71 ng/mL. The corresponding area under the curve (AUC) of MLT-SiO2-HP55 was 3.5 times higher than that of raw MLT. This finding illustrated the sustained release of MLT-SiO2-HP55. Our in vitro release and in vivo absorption studies indicated that the proposed preparation of MLT-SiO2-HP55 is an effective method to facilitate the controlled and sustained release of MLT with enhanced bioavailability.