The optoelectronic oscillator (OEO) uses an optical energy storage element to achieve high quality microwave signals which are spectrally pure. But in some applications, the stability loss and large physical size become considerable problems. To solve these problems, we present an approach of building chip-scale atomic resonator-based stabilization system for optoelectronic oscillators. This system is mainly made up of chip-scale CPT atomic clock and enhanced PLL synchronization circuits. We lock the oscillation of OEO to a high stable microwave reference which is synchronized from CPT atomic clock. In our system, we obtain a stable 3.035 GHz microwave signal with a short-term frequency instability of 2×10 -10 (1 s) and a long-term instability of 5×10 -11 (1000 s). The whole physics package of the stabilization system is 4.5 cm×4.5 cm×2 cm.