The internal nozzle flow has great influence on fuel injection and spray. This work investigates the impacts of the injection back pressure on the nozzle inner cavitation developing, especially the flow characteristic during choking process. Based on the theoretical analysis, a three-dimension numerical model is developed to investigate the details of the inner nozzle cavitation flow. The numerical model is verified by experiments on a diesel fuel system test rig under different boundary pressures, including varied injection pressure and back pressure. The investigation shows that for a given injection pressure, cavitation occurs with the drop in the back pressure. The incipient bubbles appear just at the upper corner of nozzle inlet hole, and the cavitation area continues to expand until it reaches to the nozzle outlet. The nozzle inner cavitation is divided into three periods: no cavitation period; local cavitation developing period and super cavitation period. Before the super cavitation, as the back pressure drops, bubbles at the entrance of the nozzle hole cover more area, but the average liquid velocity increases and as a result the mass flow increases. Once the liquid velocity reaches to its maximum, the cavitation of the nozzle inlet hole maintains stable, so does the vapor–liquid mixture cross section, and the effective cross section of the liquid phase is minimum; by now the super cavitation forms. Under the condition of the super cavitation, the nozzle inner flow becomes choking and the back pressure has little influence on the mass flow, but the discharge coefficient declines as the back pressure decreases. During the choking flow period, when the back pressure declines, along the nozzle hole central axis from the inlet to the outlet, the effective flow cross section maintains stable in sequence and the liquid velocity also reaches its maximum in order. Moreover, at the outlet of the nozzle hole, super cavitation induces the increase of the turbulence kinetic energy and the outlet velocity. This increased outlet velocity makes up for the loss of the contracting effective flow passage due to super cavitation, thus the total mass flow maintains the same value after choke even the back pressure decreases.