Considering the water-invaded zone caused by the invasion of fracturing fluid into the reservoir, the post-fracturing stimulated zone, water-invaded zone and main fractures of deep shale gas reservoirs were classified in detail. The seepage mathematical model under Laplace space considering the desorption of gas from the shale matrix, gas-water two-phase flow in the water-invaded zone and main fractures was established. By linearizing the model and combining the gas-water two-phase material balance equation, a semi-analytical solution method for the gas-water two-phase seepage model was formed, which was verified by numerical simulation. A method for inverting the parameters of the fracture network based on the dynamic fitting of gas-water two-phase production was formed. Finally, the production data of YH75 well in the deep shale gas reservoir of Luzhou block was fitted and inverted to analyze its modification effect. The results show that: (1) The gas-water two-phase flow of shale gas wells considering water invasion shows five flow stages, including water phase linear flow, water phase boundary-controlled flow, gas phase bilinear flow, gas phase linear flow and gas phase boundary-controlled flow; (2) The main fracture half length of YH75 well is about 90m, the permeability of the stimulated zone is at the order of 0.001mD, the thickness of the water-invaded zone is about 0.5m, and the permeability of the water-invaded zone is one order of magnitude lower than that of the stimulated zone; (3) The flow stages of the seepage model considering water-invaded zone and gas-water two-phase flow are significantly different from those of the conventional seepage model. If the water-invaded zone and gas-water two-phase flow are not considered, the predicted production in the early stage will be much higher than the field data.