A Hg-based ternary infrared nonlinear optical (NLO) material, HgGeSe, with the defect diamond-like (DL) structure was systematically investigated for the first time. The experimental results show that HgGeSe exhibits an enhanced second harmonic generation (SHG) response about 2.1 times that of the normal DL selenide AgGaSe ( d = 33 pm/V) at the particle size of 150-200 μm, as well as good phase-matchable ability. Moreover, theoretical analysis reveals that the nonbonding electrons around Se atoms in the defect DL structure make a dominant contribution to the improvement of the NLO property: d = 78.83 pm/V and Δ n = 0.11. This study highlights the promise of electronic engineering strategies and opens new avenues toward the design of new infrared NLO crystals with high performance.