Organic−inorganic hybrid nonlinear optical (NLO) crystals have been attracting increasing attention because of their unique ability to combine the structural diversity of the organic moiety and the high stability of the inorganic moiety. However, organic NLO genes are rare. Herein, a new organic NLO material gene, the 2aminopyrimidinium cation (C 4 H 6 N 3 ) + ((2AP) + ), is reported, which constructs a novel organic−inorganic hybrid (C 4 H 6 N 3 ) + (H 2 PO 3 ) − (2APP) that exhibits excellent NLO properties and thermal stability, e.g., strong second-harmonic generation (SHG) intensity (2 × KDP), large birefringence (0.225 at 589.3 nm), high laser-induced-damage threshold (1.7 × KDP), and one of the highest thermal stabilities among the metal-free-(2AP) + -containing compounds. Our first-principles theoretical studies confirm the dominant contribution of (2AP) + to optical properties. The inorganic phosphite anions well separate the (2AP) + cations to successfully eliminate the unwanted centrosymmetric trap that is induced by the dipole−dipole interactions between (2AP) + cations. Furthermore, the unique layered structure decorated by the uniformly oriented individual (2AP) + chromophores, dramatically enhances the quantum yield of purple fluorescence (Φ = 30.6%), which is 3 orders of magnitude higher than that of pure 2AP and its derivatives.