The flow stability of shape memory alloy (SMA) self-regulated cryocoolers with different orifice sizes is analyzed via theoretical calculation and experimental study. The theoretical calculation demonstrates that the smaller the orifice diameter, the more stable is the flow rate when the cryocoolers are influenced by the same disturbance factors. The change in flow rate increases linearly with the increase in orifice diameter. In the experimental investigation, two types of SMA self-regulated cryocoolers, equipped with 0.15 mm and 0.25 mm orifices, respectively, were developed. Fatigue and vibration tests were introduced as disturbance factors. The flow rates of cryocoolers were evaluated at 29 and 22 MPa. The results show that the cryocoolers with a 0.15 mm orifice have smaller flow rate variance than those with a 0.25 mm orifice. Both the theoretical and experimental results verified that narrowing the diameter of the orifice is conducive to the flow stability of SMA self-regulated cryocoolers.