Marine shales in southern China experiences multiple complex tectonic movements, which highly affects shale pore characteristics and pore evolution. The effects of tectonic deformation on nanopore structure and petrophysical properties of organic shales remain unclear. Three ductile deformed shale samples were collected and analyzed through an integrated experiment procedure for a comparative research against undeformed shale samples. Field emission-Scanning electron microscopy (FE-SEM), low pressure N2 and CO2 adsorption and mercury injection porosimetry (MIP) analyses were performed to characterize pore structure of the shales. The results reveal that the mineral compositions of these shale samples are controlled by sedimentary environment and source and exhibits no obvious relationship with tectonic deformation. With increasing deformation degree, the micropore proportion gradually decreases (from 17% to 6%), and the macropore proportion increases from 16% to more than 20%. Micropore volumes and proportion in the fold core samples are the smallest (4.2 × 10−3 cm3/g and 6.3%) and account for only one-third of the undeformed shale values, while the meso- and macropore values are larger-1.2 times those of the undeformed shale values. The evolution characteristics and deformation modes of organic matter (OM), interparticle (interP) and intraparticle (intraP) pores and microfractures under ductile deformation were examined. All pore types become interconnected during deformation and form microfractures ranging from a few nanometers to tens of microns, which is the main reason for the enhanced shale connectivity caused by deformation. Under the same porosity conditions, the deformed shale permeability is much higher than the undeformed shale permeability, and stronger deformation corresponds to higher permeability. The fold core permeability is generally higher than the limb permeability and exceeds 30 times. The different ductile deformation positions were divided into five levels, and the corresponding reservoir quality was evaluated. This study is of great significance to better understand the pore structure evolution process for shale exploration and development under tectonic deformation.