A smooth end face is the critical factor for the application of photonic crystal fiber (PCF) to enhance coupling efficiency. A number of air holes distributed on the cladding make the surface a discontinuous structure. For the sake of acquiring a high-quality end surface of PCF, this paper proposes a detailed study first on dynamics simulation of the grinding process of PCF using a finite element model with a verification experiment later. To facilitate the calculation, the grinding is simplified as a single grain to cut the material on the location between two holes. The process of material removal is analyzed on the basis of force curve obtained by changing the cutting depth and position, respectively. Theoretical and experimental results illustrate that the earliest material collapse occurs on the rim of the air hole, and brittle cracks extend along circumferential and axial direction of the hole; the damage on the edge of the hole is more severe with the increment of grain tip radius and cutting depth. Keeping the grinding force stable can achieve the process in the ductile regime, and a smooth surface can be obtained by polishing with abrasive paper of fine grit.