This dataset compiles physical and chemical characteristics of individual polymetallic nodules collected in the Clarion–Clipperton Zone (equatorial NE Pacific) during the campaigns GSRNOD21, Mangan2021, and SO295, with each sample linked to a unique polymetallic nodule identifier and full event metadata (station/event label, UTC date/time, latitude/longitude, water depth/elevation, sampling device, and region). For each nodule, we report (i) morphometrics (length, width, height, ellipsoid volume, and size category), (ii) surface/porosity structure quantified as crevice size statistics and crevice counts per analyzed area, (iii) internal and external crack diameters measured from image-based observations in multiple sections (central/top/bottom) across size classes, and (iv) elemental composition from SEM-based microanalytical measurements reported as weight % and atom % for a suite of elements, together with contextual descriptors (sediment depth, feature type, and measurement type).