Phosphates usually have shorter ultraviolet (UV) absorption edges and are ideal for deep-UV nonlinear optical (NLO) applications. The introduction of d0 transition metal cation Mo6+ into phosphates can facilitate to increase the distortion of the crystal structure and therefore it is easy to obtain the noncentrosymmetric (NCS) compounds, which are expected for NLO materials. In the work, the crystals of an ammonium molybdenophosphate chloride [NH4]12[(Mo2)2O(HPO4)2]4[PO4]Cl·0.5H2O (AMPC) were grown by hydrothermal method. The second harmonic generation (SHG) of the compound exhibits 0.3 × KH2PO4 (KDP) at 1064 nm radiation and the cutoff edge of it is about 230 nm. The crystal structure is consist of unique [Mo4P4O32H4]16− units and further to form layer two-dimensional (2D) structure. The first-principles electronic structure calculations show that the NLO response of it mainly comes from the Mo-O units. We also studied UV–vis-NIR diffuse reflectance, infrared spectrum and thermal properties of the compound. Additional, by the investigation of similar phosphomolybdates, we found that they have high ratios of NCS crystal structures about 39%.