Spinel has outstanding optical performances and mechanical performances, and it is suitable material for infrared window and dome. But it is extremely difficult to machine spinel with high accuracy, especially in the machining process with compliant polishing tools, grain profiles will appear on the machined surface, which will result in the deterioration for machining accuracy, surface quality and optical performance. In this paper, analyzing the microscopic figure of spinel in the process of complaint polishing and founding the gradient change obviously on the edge of the grain profile, which has significant influence on the surface roughness. The spinel substrates are separately polished by using pitch tool, polyurethane tool and magnetorheological fluid, the values of surface roughness are respectively Ra 2.3nm, Ra 8.5nm and Ra 64.6nm, and the corresponding characteristic scales of grain profile are 180μm~200μm, 160μm~200μm and 200μm~250μm. Furthermore, the peak value of grain profile is proportional to the polishing tool flexibility, inverse proportional to the rigidity and the size of polishing powder, and the flexibility expression for polishing tool is given on the conditions of different machining parameters. On this basis, the high accuracy and ultra smooth surface of the spinel are obtained by the optimum polishing conditions.