In this work, cubic garnet-type AY2Al4GeO12 (A = Ca, Mg) ceramics were synthesized by a solid-state reaction method. XRD detected that CYAG was a single-phase, and the secondary phase existed in the MYAG. SEM, density, and dielectric properties results indicate that the optimum sintering temperature of CYAG and MYAG ceramics is 1550 °C, the CYAG and MYAG ceramics exhibited the best microwave dielectric properties of εr = 8.94, Q×f = 93805 GHz, τf = −48 ppm/°C and εr = 7.06, Q×f = 30549 GHz, τf = −26.55 ppm/°C, respectively. Rietveld refinement, Raman and XPS confirmed that the significant difference in dielectric properties is related to the secondary phase, structural disorder and oxygen vacancy. The relationship between the Q×f and lattice vibration are discussed. τf is explained by oxygen bond valence. The influence of bond characteristics on dielectric properties was analyzed. The reported microwave ceramics are expected to be used as substrate materials in the millimeter wave band.