Deep metamorphic rock reservoir permeability prediction faced great challenge due to strong heterogeneity. Fractures were widely developed, but the traditional models did not involve into the contribution of fractures. To establish an effective model to predict permeability, parameters related to fracture needed to be taken into account. In this study, taking the Archaeozoic Formation in BZ 19-6 Region - a typical deep metamorphic rock reservoir and located in southwestern Bohai Bay Basin - as an example, the porosity frequency spectra were first extracted from electrical imaging logging, and relationships between the shape of porosity frequency spectrum and rock pore structure were analyzed. Two parameters, which were defined as the logarithmic mean (φgm) and standard deviation between two golden section points (φgsr), were used to reflect the main position and wide of porosity frequency spectrum, and a novel model to predict permeability was established. After the target formations were classified into two types based on the difference of pore type and pore-fracture configuration relationship, the involved model coefficients were calibrated. Consecutive permeability curves were derived from our raised model in the intervals with which porosity frequency spectra were acquired. Comparisons of predicting permeabilities with core-derived results illustrated that this proposed model was much reasonable, and the resolution of predicted permeability curve was high. Except for the deep metamorphic rock reservoirs, the estimated model could be widely used in other types of formations (e.g., volcanic rock reservoirs, carbonate rock reservoirs) where secondary pores were developed.