Directly solving the full electron-nuclear Schrödinger equation remains one of the grand challenges in quantum mechanics. Here, we propose a quantum-chemically motivated orbital-based neural network wavefunction ansatz with explicit many-body electron-electron correlation terms, with parameters depending on the entire electron-nuclear configuration, enabling an accurate description of strongly correlated and/or multi-reference electronic structures by a single Slater-determinant across a broad nuclear configuration space. To train this wavefunction, we further develop an efficient hybrid optimization strategy that combines the variational Monte Carlo technique with local-energy constraints, mitigating the intrinsic sampling bias of the former and considerably reducing the statistical error. These advances are embedded in a unified neural network framework, Schrödinger, enabling the determination of globally accurate potential energy surfaces with a single training for systems ranging from strongly correlated diatomic molecules, triatomic reactions containing conical intersections, to polyatomic multi-reference molecules. This work offers a practical machine-learning tool for solving the electron-nuclear Schrödinger equation and capturing full quantum effects beyond the Born-Oppenheimer approximation.