Microwave irradiation stimulation is proposed as a new approach to improve shale oil and gas recovery. Since shale oil and gas recovery is controlled by pore connectivity, this work investigated the effects of microwave irradiation on the pore connectivity of shales with different maturities. In this study, we first characterized the initial pore connectivity of shale samples by the combination of (ultra) small-angle neutron scattering and mercury injection capillary pressure. Then, (ultra) small-angle neutron scattering results were used to compare the pore size distribution of shale samples under different microwave treatment times. The experiment results show that microwave treatment can reduce fine pore networks (<10 nm) and form large pore-fracture systems (>10 nm) for shale oil samples. In addition, the number density of pores for shale gas samples exhibited a decreasing trend with the time of the microwave treatment, indicating that many pores expanded and connected. Therefore, microwave irradiation stimulation can improve the pore connectivity and create new flow paths for oil and gas from the shale matrix to the fracture system. Meanwhile, the high content of pyrite and clay will enhance the microwave adsorption ability of shale. This study establishes the environmentally friendly microwave irradiation used in tandem with hydraulic fracturing as an efficient method of improving shale oil and gas recovery.