Anchor loss is usually the most significant energy loss factor in Micro-Electro-Mechanical Systems (MEMS) resonators, which seriously hinders the application of MEMS resonators in wireless communication. This paper proposes a cross-section connection phononic crystal (SCC-PnC), which can be used for MEMS resonators of various overtone modes. First, using the finite element method to study the frequency characteristics and delay line of the SCC-PnC band, the SCC-PnC has an ultra-wide bandgap of 56.6–269.6 MHz. Next, the effects of the height h and the position h₁ of the structural parameters of the small cross-connected plate on the band gap are studied, and it is found that h is more sensitive to the width of the band gap. Further, the SCC-PnC was implanted into the piezoelectric MEMS resonator, and the admittance and insertion loss curves were obtained. The results show that when the arrangement of 4 × 7 SCC-PnC plates is adopted, the anchor quality factors of the third-order overtone, fifth-order overtone, and seventh-order overtone MEMS resonators are increased by 1656 times, 2027 times, and 16 times, respectively.