Revealing the ultrasonic cutting mechanism of honeycomb composite is important for determining the acoustic parameters of the ultrasonic system and selecting the parameters of the cutting process. Understanding more details of the stress on the cell wall from ultrasonic vibrating tool and the conditions for cell wall breakage is essential to study the machining mechanism. According to the evolution of contact state between the straight edge cutter and the honeycomb cell wall in a cycle, the cutting force acting on the cell wall is divided into three stages: transverse cutting load action, longitudinal cutting load action, and no cutting load action. The cell wall deflection and stress equations under transverse cutting load were established by applying elastic thin plate small deflection theory. The deformation and fracture characteristics of the honeycomb cell wall were analyzed by combining the analytical and the finite element model. The results showed that the ultrasonic vibration of the cutter greatly improved the stiffening effect of the cell wall and its fracture was caused by the deflection under the transverse cutting load, which exceeded the maximum allowable deformation after local stiffening. In addition, with only longitudinal cutting load, it was difficult to break the critical buckling state that leads to cell wall fracture.