Two-dimensional aluminophosphate is an important precursor of phosphate-based zeolites; a new Sun Yat-sen University No. 6 (SYSU-6) with |Hada|2[Al2(HPO4)(PO4)2] has been synthesized in the hydrothermal synthesis with organic structure-directing agent (OSDA) of N,N,3,5-tetramethyladamantan-1-amine. In this paper, SYSU-6 is characterized by single-crystal/powder X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray analysis, transmission electron microscopy, infrared and UV Raman spectroscopy, solid-state 27Al, 31P and 13C magic angle spinning (MAS) NMR spectra, and elemental analysis. The single-crystal X-ray diffraction structure indicates that SYSU-6 crystallized in the space group P21/n, with a = 8.4119(3), b = 36.9876(12), c = 12.5674(3), α = 90°, β = 108.6770(10)°, γ = 90°, V = 3704.3(2) Å3, Z = 4, R = 5.12%, for 8515 observed data (I > 2σ(I)). The structure has a new 4,12-ring layer framework topology linked by alternating AlO4 and PO4 tetrahedra. The organic molecules reside between the layers and are hydrogen-bonded to the inorganic framework. The new type of layer provides a greater opportunity to construct zeolite with novel topology.