Irradiation effect of low-energy nitrogen ion beam on amorphous carbon nitride (a-CNx) thin films has been investigated. The a-CNx films were prepared on silicon single crystal substrates by hot carbon-filament chemical vapor deposition (HFCVD). After deposition, the CNx films were irradiated by a nitrogen ion beam with energy from 0.1 to 2.0 keV. Irradiation effect on the film microstructure and composition was studied by SEM and XPS, focusing on the effect of nitrogen ion beam energy. Surface and cross sectional observations by SEM reveal that the as-deposited films show a densely distributed columnar structure and the films change to be a sparsely distributed cone-like structure after irradiation. It is also found that 2.0 keV ions skeltonize the films more clearly than 0.1 kev ions. Depth profiles of nitrogen in the films observed by XPS show that nitrogen absorption into films is more prominent after irradiation by 0.1 keV nitrogen ions than 2.0 keV ions.