The intergranular glassy film (IGF) composed of silicon oxynitride in a Si3N4 ceramic material has been studied by molecular dynamics calculations. Structural analyses showed that the presence of an IGF having both nitrogen and oxygen reduces the number of dangling bonds at the junction between the IGF and adjacent Si3N4 grains, which reduces the interface energy at the grain boundary. More dangling bonds were generated at the junction when the N/(N + O) ratio of the IGF was decreased due to the larger chemical and structural mismatch between the IGF and the adjacent grain. On the other hand, the increase in the N/(N + O) ratio of the IGF caused a greater energy penalty in the IGF. The balance of these two contributions should determine the chemistry of the IGF.