Precise manipulation of skyrmion nucleation in microscale or nanoscale areas of thin films is a critical issue in developing high-efficient skyrmionic memories and logic devices. Presently, the mainstream controlling strategies focus on the application of external stimuli to tailor the intrinsic attributes of charge, spin, and lattice. This work reports effective skyrmion manipulation by controllably modifying the lattice defect through ion implantation, which is potentially compatible with large-scale integrated circuit technology. By implanting an appropriate dose of nitrogen ions into a Pt/Co/Ta multilayer film, the defect density was effectively enhanced to induce an apparent modulation of magnetic anisotropy, consequently boosting the skyrmion nucleation. Furthermore, the local control of skyrmions in microscale areas of the macroscopic film was realized by combining the ion implantation with micromachining technology, demonstrating a potential application in both binary storage and multistate storage. These findings provide a new approach to advancing the functionalization and application of skyrmionic devices.