Based on the principle of low-temperature deposition manufacturing (LDM), the feeding velocity can be regulated by air pressure. During the whole forming process, the stability of feeding has directly impact on the forming result of scaffold. Under the matching condition of optimal velocity, an appropriate extrusion velocity is the key factor to fabricate perfect structure of macro pore, which avoids collapse between layers and over accumulation. Based system identification theory, this paper builds the model of pressure and extrusion velocity by analyzing the process of Pneumatic material feeding, and then designs PI controller by simulation to guarantee the stability and rapidity. Experiments verifies that the phenomenon of over accumulation and less-lap caused by feeding pressure has been solved at some extent by regulating air inflate and exhaust valve. Conclusion shows the effective control of feeding velocity has great significance for improving the technical level of the bionic bone scaffold fabrication process and fulfilling the automation of bone scaffold molding equipment.