Abstract: The low permeability conglomerate reservoir in the Lower Triassic Baikouquan formation of Mahu sag, Junggar basin is characterized by complex reservoir lithology, complicated clay minerals and serious heterogeneity, so it is difficult to accurately characterize the effective porosity of the conglomerate reservoir with current logging methods. Considering that the clay mineral content is the controlling factor of reservoir physical properties, the paper uses the difference between neutron logging porosity and NMR logging porosity and clay mineral content obtained from core analysis to establish a clay mineral content characterization model; then uses clay bound water porosity and clay mineral content obtained from core analysis to establish a clay bound water porosity characterization model, based on which the effective porosity can be obtained by NMR porosity minus clay bound water porosity. The actual application of the method in 19 exploration wells in the study area shows that the relative error of effective porosity is only 6.8%, indicating that good effect has been gained by using the method, which could provide a new technological means for effective porosity evaluation with NMR logging data