Control rod hydraulic drive system (CRHDS) is a new built-in control rod drive technology developed by Tsinghua University for NHR200-II. Hydraulic cylinder is the key driving component of CRHDS. Its action may cause water hammer processes in the drive circuit and impact the system. The hydraulic cylinder parameters have significant effects on the transient flow process. The composition and operational principle of CRHDS are analyzed, and thermal experimental studies of different hydraulic cylinders were carried out. A theoretical model of the filling process is developed, and the calculated results agree well with experimental results. Based on this model, the filling processes of hydraulic cylinders with different parameters were analyzed. The results show that an increase in the hydraulic cylinder load corresponds to a rise in the peak water hammer pressure and a delay of the triggering moment. An increase in the cross-sectional area of the inner sleeve leads to a decrease in the peak pressure of the water hammer and an earlier triggering moment. Additionally, the spring elasticity coefficient and the leakage coefficient of the hydraulic cylinder also affect the transient filling flow process. The findings of this study can provide guidance for the design optimization and vibration reduction of the CRHDS.