In this paper, a compact and high-selectivity RF filter based on MEMS technique is designed. Compared with the traditional micro-electro-mechanical system(MEMS)filter, the proposed filter adopts a stepped impedance resonator (SIR) to reduce the size of device, and uses field distribution of the resonator to form a compact cross-coupling which eliminates the traditional flying rod and structure, and the compact layout of the device is achieved while improving the selectivity of the filter. The surface metal resonator cavity of the filter is grounded by the metalized through silicon via, forming a quarter-wavelength resonant structure. The filter with different performance and structural parameters are designed and analyzed, and simulated by the three-dimensional electromagnetic simulation software. The results show that the filter size is 10 mm×10 mm×0.4 mm, the stationary wave is less than 1.3 dB, the insertion loss is less than 3.5 dB, and the out-of-band rejection is larger than 30 dB at 2.5-2.7 GHz and 3.4-3.5 GHz.