Ion-beam irradiation of poly(methylphenylsilane) (PMPS) is shown to cause cross-linking reactions, leading to the formation of a polymer gel containing cylindrical nanostructures of regular length and thickness. The spatial distribution of cross-links of polymer molecules is found to be governed by the deposited energy density in an ion track. The radial variation in dose along each ion track results in the formation of cylindrical structures with a radius of 1-12 nm. These cylindrical structures are well visualized by atomic force microscopy as wormlike structures (nanowires). The total volume of the crosslinked polymer gel can be represented by this cylindrical radially varying scheme of cross-link distribution well. As the cross-linking reaction efficiency estimated by conventional statistical theories of polymer gelation overestimate the dependence of the efficiency on the chain length of the polymers, a new formalism is derived considering the dependence of the nanowire size on the chain length, the linear energy transfer of the ion beam, the radial dose distribution in ion tracks, and the global chain configuration of polymers. The resultant model provides a better representation of ion-beam-induced gelation of polymers. The present results also demonstrate the potential utility of this technique for single-particle fabrication of nanostructures with subnanometer spatial resolution.