Microstructure is important to the development of energy devices with high performance. In this work, a three-dimensional Si-based metal-insulator-metal (MIM) capacitor has been reported, which is fabricated by microelectromechanical systems (MEMS) technology. Area enlargement is achieved by forming deep trenches in a silicon substrate using the deep reactive ion etching method. The results indicate that an area of 2.45 × 103 mm2 can be realized in the deep trench structure with a high aspect ratio of 30:1. Subsequently, a dielectric Al2O3 layer and electrode W/TiN layers are deposited by atomic layer deposition. The obtained capacitor has superior performance, such as a high breakdown voltage (34.1 V), a moderate energy density (≥1.23 mJ/cm2) per unit planar area, a high breakdown electric field (6.1 ± 0.1 MV/cm), a low leakage current (10−7 A/cm2 at 22.5 V), and a low quadratic voltage coefficient of capacitance (VCC) (≤63.1 ppm/V2). In addition, the device’s performance has been theoretically examined. The results show that the high energy supply and small leakage current can be attributed to the Poole–Frenkel emission in the high-field region and the trap-assisted tunneling in the low-field region. The reported capacitor has potential application as a secondary power supply.