The morphology and mechanism of lithium niobate (LiNbO3) crystal ablated by a femtosecond laser pulse have been studied. The ablated spots and surface diffraction grating have been examined by means of scanning electron microscopy (SEM) and atom force microscopy (AFM). Sub-diffraction limit spots in LiNbO3 crystal ablated by femtosecond laser have been obtained. The diameters of ablation spots are 400nm and 800nm when 170nJ single pulse and 100nJ 17 pulses are used, respectively. There are ripples with about 200nm periodic on the bottom surfaces of the spots at low laser energy. The result shows that the sub-diffraction limit structures may be formed by the multi-photon excitation, and the femtosecond laser ablation is an innovative tool for manufacturing LiNbO3-based optical devices.