Radiation-tolerant materials are in great demand for safe operation and advancement of nuclear and aerospace systems. Nanostructuring is a key strategy to improve the radiation tolerance of materials. SiOC polymer-derived ceramics (PDCs) are unique synthetic nanocomposites consisting of β-SiC nanocrystals and turbostratic graphite distributed in amorphous SiOC matrix, which are "all-rounder" materials for many advanced structural and functional applications. Radiation effects in the crystalline−amorphous system have been investigated in detail by experiments and molecular dynamics (MD) simulations. The results indicate that the amorphous SiOC structure retains amorphous accompanied by redistribution of the Si-containing tetrahedra. The graphite is shown to amorphize more easily than β-SiC nanocrystals under the same irradiation condition. The sample richer in oxygen, namely, containing more amorphous SiOC, shows less disordering of graphite, resulting from greater mitigation of radiation damage by the amorphous phase as efficient sinks. This study provides details of the microstructure evolution of SiOC PDCs under ion irradiation, as well as insights for the design and development of advanced ion damage-resistant materials.