Owing to wide infrared (IR) transparency ranges, high laser damage thresholds, and being easy to grow in open air, germanates are emerging as promising mid-infrared (mid-IR) nonlinear optical (NLO) materials. However, the germanates as NLO materials have not been investigated comprehensively and the crystals with large second harmonic generation (SHG) response have not been identified. Herein, we used the first-principles high-throughput screening pipeline for NLO materials to search for excellent NLO crystals from germanates collected in the inorganic crystal structure database. After two steps of screening, three crystals are picked out from 128 structures based on their predicted energy gaps, birefringences, and SHG coefficients. Subsequently, the three germanates are synthesized and measured. The results show that Pb3Ga2Ge4O14 and Ba2TiGe2O8 exhibit a wide energy gap (>3.1 eV) and a strong phase-matchable SHG intensity that are comparable to the benchmark AgGaS2 (0.8 and 1.2 × AgGaS2, respectively). In addition, the statistical analyses of different categories classified according to their cations show that the d0-transition metal and lone pair cations are more conducive to achieving a larger SHG response and birefringence compared to other cations in germanates. It gives a guideline for exploring new mid-IR NLO materials.