Direct observations and measurements on deformational and sedimentary structures, fluid activities, physical properties, and chemical compositions of core samples from accretionary prisms at different pressure and temperature settings are critical to understanding seismogenic mechanisms of subduction zone earthquakes. Based on core measurements from IODP expedition 316 of the first stage of the NanTroSEIZE program, we analyze deformational and sedimentary structures at the core scale at four sites, C0004, C0006, C0007 and C0008, at the toe the accretionary prism along the Nankai Trough. We also discuss the relationships between structures at the core scale and large scale structures like splay fault and frontal thrust fault. It is found that thrusting deformation in the accretionary prism is accommodated not only by deformation within large-scale thrusting zones, but also by deformation along secondary thrusts and potentially more importantly along core-scale structures such as micro-faults and deformation bands. The consistencies in dipping angles between large scale thrusts and core-scale structures indicate that structures at different scales are formed under a unified stress field within the accretionary prism. At the shallow part of the accretionary prism, high angle normal faults dominate, showing extensional stress field, and beddings and fissilities from core samples show trends and high dips consistent with those estimated from seismic stratigraphy and regional structures. At deeper parts, particularly near the large scale thrusts, faults of all types, joints and deformation bands are common features, and beddings and fissilities show vertiginous attitudes controlled preferably more by large scale thrusting deformation.