Quantum transport calculations are essential for understanding and designing nanoelectronic devices, yet the trade-off between accuracy and computational efficiency has long limited their practical applications. We present a general framework that combines the deep learning tight-binding Hamiltonian (DeePTB) approach with the non-equilibrium Green's Function (NEGF) method, enabling efficient quantum transport calculations while maintaining first-principles accuracy. We demonstrate the capabilities of the DeePTB-NEGF framework through two representative applications: comprehensive simulation of break junction systems, where conductance histograms show good agreement with experimental measurements in both metallic contact and single-molecule junction cases; and simulation of carbon nanotube field effect transistors through self-consistent NEGF-Poisson calculations, capturing essential physics including the electrostatic potential and transfer characteristic curves under finite bias conditions. This framework bridges the gap between first-principles accuracy and computational efficiency, providing a powerful tool for high-throughput quantum transport simulations across different scales in nanoelectronics.