In this article, a two-dimensional (2D) honeycomb lattice phononic crystal (PnC) based micro-oven with large bandgap is introduced to be integrated with piezoelectric microelectromechanical systems (MEMS) resonator to reduce anchor loss for timing applications. Finite element method (FEM) analysis and experimental measurement were performed to verify that the proposed PnC micro-oven design gives advantage in quality factor (Q). The measurement results demonstrate that the resonator with 2D honeycomb lattice PnC micro-oven shows a repeatable 1.7 times improvement of average Q compared with the bare one. The resonator with micro-oven control was further measured for frequency stability. The proposed piezoelectric micro-oven-controlled MEMS resonator achieves a frequency stability of less than ±10 ppb in a stable environment, which indicates promising potential for application in high-end timing field.