The crystal stock defect was formed in growing for a long time (22 h) of plate type Ib large diamond single crystals from the NiMnCo−C system at high pressure and high temperature (HPHT). The existence of crystal stock defect has great influence on the synthesis of high quality and large size diamond single crystal. In this paper, the effects of crystal growth rate and catalyst components on diamond crystal stock defects are studied. Firstly, the results show that the growth rate of diamond crystals is closely related to the generating of diamond crystal stock. This defect can be eliminated as the growth rate of diamond crystal synthesized with NiMnCo catalyst is reduced to less than 3 mg/h. Secondly, the composition of the catalyst also affects the formation of the crystal stock. High viscous FeNi catalyst is used to grow high quality large single crystals of diamonds at a growth rate of 3.18 mg/h for a long time (22 h). Thirdly, the effect of catalyst composition on diamond crystal stock was analyzed by testing the micro-morphology and nitrogen content of diamond. It can be shown from the results by scanning electron microscopy (SEM) that the surface of crystals synthesized with low-viscosity catalyst is rough, while it synthesized with high-viscosity catalyst is smooth. It was found from the test results of micro Fourier-transform infrared spectroscopy (FTIR) that the content of nitrogen in the crystals synthesized with FeNi catalyst was much lower than that in the crystals synthesized with NiMnCo. FeNi catalyst can effectively avoid the crystal stock, and is more suitable for the growth of large-size and high-quality diamond single crystal. Changing the composition of the catalyst is an effective way to avoid the crystal stock phenomenon.