Developing superior deep-ultraviolet (deep-UV) nonlinear optical (NLO) materials is a great challenge because of the contradiction between deep-UV transparency and enhanced second harmonic generation (SHG), especially for deep-UV NLO phosphates in which the constituent P–O groups have relatively small microscopic SHG coefficients. Here we report a new noncentrosymmetric phosphate Cs2LiPO4 (I), whose crystal structure consists of [LiPO4]∞ layered structural units with a novel honeycomb-like topology. As compared with the benchmark deep-UV NLO material KBe2BO3F2, I is beryllium-free, and it is relatively easy to grow its large single crystals because of its congruent melting. Furthermore, it not only is deep-UV transparent but also exhibits an unexpectedly enhanced SHG response of 1.8 × KH2PO4 that hits a new high in deep-UV NLO phosphates. These results demonstrate that I satisfies the key requirements of being a promising deep-UV NLO candidate. Theory calculations and structural analysis reveal that the enhanced SHG response can be attributed to the honeycomb-like topological structure, which endows the constituent [PO4]3– monomers of I with an aligned arrangement and as a result a favorable superposition of their microscopic SHG coefficients. These findings may provide useful insights into the development of both deep-UV NLO materials and honeycomb-like topological structures.