Breakdown of diffuser flow was often observed in our scramjet engine tests. This facility operation may damage the engine wind-tunnel and should be prevented. An one-dimensional analysis was applied to the diffuser flow to identify the causes of the flow breakdown. All the losses and gains by engine and friction loss in the diffuser were represented by point-sources of mass, momentum and energy. The thermal choking condition was calculated by uses of a chemical equilibrium code. The fuel rates causing the flow-choking successfully reproduced the limit fuel rates observed in our tests. Inlet-unstart of engine lost the ejector-pumping effect in the diffuser system to trigger the flow choking. The choking was also promoted by the drag of the gas sampling rakes. The choking in diffuser flow and the engine unstart may couple each other to cause hysteresis in the diffuser breakdown, which was also experienced in our tests. A rocket-based, combined-cycle (RBCC) engine will be tested under the Mach 4 condition. The engine easily causes the choking of diffuser because of the large propellant supply rates and the relatively-low specific impulse. Operation of the wind-tunnel was discussed to control the flow choking in the tests.