To design new nonlinear optical (NLO) crystals efficiently, mixing two or more types of functional groups is a favored strategy. Herein, by combining two types of planar π-conjugate groups, triangular (BO3)3- and square (C4O4)2-, the new lithium borate-squarate composite NLO crystal Li2(C4O4)(H3BO3)(H2O)4·H3BO3 was synthesized, featuring a layered structure. This crystal exhibits a moderate second harmonic generation (SHG) response of 1.1 × KDP and a large birefringence of 0.267@1064 nm. Theoretical calculations demonstrate that the synergistic effect of the two types of groups is responsible for its optical performance. This work also enriches the currently scarce borate-squarate composite compound system.