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Abstract Integrated photon-pair sources are crucial for scalable photonic quantum systems. Thin-film lithium niobate is a promising platform for on-chip photon-pair generation through spontaneous parametric down-conversion (SPDC). However, the device implementation faces practical challenges. Periodically poled lithium niobate (PPLN), despite enabling flexible quasi-phase matching, suffers from poor fabrication reliability and device repeatability, while conventional modal phase matching (MPM) methods yield limited efficiencies due to inadequate mode overlaps. Here, we introduce a layer-poled lithium niobate (LPLN) nanophotonic waveguide for efficient photon-pair generation. It leverages layer-wise polarity inversion through electrical poling to break spatial symmetry and significantly enhance nonlinear interactions for MPM, achieving a notable normalized second-harmonic generation (SHG) conversion efficiency of 4615% W−1cm−2. Through a cascaded SHG and SPDC process, we demonstrate photon-pair generation with a normalized brightness of 3.1 × 106 Hz nm−1 mW−2 in a 3.3 mm long LPLN waveguide, surpassing existing on-chip sources under similar operating configurations. Crucially, our LPLN waveguides offer enhanced fabrication reliability and reduced sensitivity to geometric variations and temperature fluctuations compared to PPLN devices. We expect LPLN to become a promising solution for on-chip nonlinear wavelength conversion and non-classical light generation, with immediate applications in quantum communication, networking, and on-chip photonic quantum information processing.