This paper introduces a chip-level oven-controlled system for improving the temperature stability of MEMS resonators wherein we designed the resonator and the micro-hotplate using MEMS technology, then bounding them in a package shell at the chip level. The resonator is transduced by AlN film, and its temperature is monitored by temperature-sensing resistors on both sides. The designed micro-hotplate is placed at the bottom of the resonator chip as a heater and insulated by airgel. The PID pulse width modulation (PWM) circuit controls the heater according to the temperature detection result to provide a constant temperature for the resonator. The proposed oven-controlled MEMS resonator (OCMR) exhibits a frequency drift of 3.5 ppm. Compared with the previously reported similar methods, first, the OCMR structure using airgel combined with a micro-hotplate is proposed for the first time, and the working temperature is extended from 85 °C to 125 °C. Second, our work does not require redesign or additional constraints on the MEMS resonator, so the proposed structure is more general and can be practically applied to other MEMS devices that require temperature control.