Powder engine is one kind of new concept engines with multiple ignition capability and thrust modulation function. Powder filling is an important process of the powder engine tests. The powder pneumatic filling experiments were carried out to investigate the effects of the filling position of the powder collection box and the mass flow rate of fluidization gas on the stability and performance of powder pneumatic filling. It’s found that large mass flow rate of fluidization gas contributes to stability of powder pneumatic filling, but its volume efficiency of powder filling is the lowest, only 68.1%, but it’s 93.9% when the mass flow rate of fluidization gas is small. Compared with the vertical inlet of end cap, tangential inlet on the cylinder wall makes the powder uniformity better. In the pneumatic filling mode, the powder bulk density in the collection box is greater than the bulk density in the powder tank. In addition, the mass of powder calculated by position displacement is always larger than the mass of powder measured by the electronic balance. It indicates powder bulk density in tank is constantly changing during the powder pneumatic filling experiments. The actual powder bulk density in the powder tank is calculated by a model established in this paper, it’s found that when the mass flow rate of fluidization gas is low, the bulk density of the powder in the tank is increased first and then decreased, and the final bulk density is less than the initial value. While the mass flow rate of fluidization gas is high, powder bulk density in the tank is first increased, then decreased, then increased and then decreased, and the final bulk density is greater than the initial value. The compression mechanism of powder bulk density in the tank is similar to the motion law of the damper spring vibrator when it is forced to vibrate. It can be described by the damped second-order system response function. When the mass flow rate of fluidization gas is small, the damping coefficient of the system is smaller. While the mass flow rate of fluidization gas is large, the damping coefficient is larger and is variable.