Natural fractures dominate fracturing effects and well production. Conventional fracturing fails to fully activate multi-scale fractures, and most simulations adopt homogeneous rock assumptions, lacking systematic analysis on fracture propagation and seepage evolution in heterogeneous fractured formations, while the natural fracture activation mechanism of pulsed fracturing remains unclear. This work constructs a pulsed fracturing model for heterogeneous fractured rock to simulate fracture growth and permeability evolution in intact rock and formations with various fracture attitudes, revealing the coupled laws of fracture propagation and seepage change. Results show rock mechanical heterogeneity determines fracture network complexity in intact rock; pulsed loading slows main fracture breakthrough and stimulates microcracks, creating a near-well dense and far-well sparse fracture distribution. Single-orientation fractures drive directional asymmetric fracture extension following near-weak-zone priority, with matrix heterogeneity merely causing local fracture deflection. Multi-orientation fractures display layered activation: low-angle and near-well fractures initiate first, and cross-fracture interactions raise network complexity and coverage. Fracture growth is jointly governed by weak bedding, pulse fatigue damage and matrix properties. Pulsed fracturing achieves remote non-contact activation of natural fractures, with fracture-permeability evolution showing strong spatiotemporal coupling; main fracture breakthrough triggers abrupt permeability growth. Serving as both mechanical weak planes and preferential flow paths, natural fractures build composite seepage systems of main channels and micro flow zones. This study provides theoretical support for parameter optimization and efficient permeability improvement in fractured reservoirs.