Recent developments in nanotechnologies have highlighted the demand for multi-dimensional, cross-scale and variable-depth nanoscale structures for applications such as nanofluidic chips, nanosensors, nanoelectronics and many more. Therefore, the implementation and system of cross-scale and variable-depth nanomanufacturing is the core of advanced nanotechnologies. Among all of the current methods, nano scratching is the easiest and most flexible approach with the advantages of low cost and simple machining procedures. In this work, a three-dimensional piezoelectric manufacturing system (PMS) based on a self-developed four-degree-of-freedom (4-DOF) inchworm piezoelectric platform is proposed for implementation of cross-scale and variable-depth nano scratching. Based on the PMS, effects of the scratching parameters such as exciting voltage and frequency on scratching depth and quality are discussed. In addition, the scratching experiments were successfully performed and achieved the nanoscale depth variation of the grooves, nesting rectangles, and concentric circles using the multi-DOF and cross-scale output characteristics of the proposed 4-DOF piezoelectric platform. To sum up, the PMS based on the 4-DOF inchworm piezoelectric platform has potential applications in the fields of machining three-dimensional nanostructures within millimeter scale.