One of the most effective ways to realize multi-mode and high-performance matching operation of rocket-based combined cycle (RBCC) engine is to adopt a variable geometry combustor. In this study, direct-connect experiments and three-dimensional numerical simulations were used to investigate the matching characteristics between the isolator and the geometric throat of the variable geometry rocket-based combined cycle combustor under Ma 6 condition. The influences of equivalence ratio and geometric throat height variations on the combustor matching characteristics were obtained. The study results show that: (1) The pressure in the combustor and the outlet pressure of the isolator increase gradually with the increase of equivalence ratio, which causes the pre-combustion shock train position in the isolator to move forward gradually. Meanwhile, the combined injection of secondary fuel with the isolator and the pylon is beneficial to the improvement of combustor pressure, thus further improving the engine performance. (2) Different geometric throat heights have a substantial impact on the isolator and combustor matching when the equivalent ratio of the combustor is fixed. Under the conditions of Ma 6 operating at an altitude of 24 km inflow, the starting position of the pre-combustion shock train in the isolator is precisely at the isolator entrance, and the corresponding geometric throat height is 2.10H. The isolator and the combustor can complete matching operation at this point which the geometric throat height is the minimal throat height for Equivalent ratio = 1.0. (3) The reduction in geometric throat height can result in an increase in combustor pressure but a loss in combustor heat release and combustion efficiency of fuel combustion, which are reduced by 21.1% and 7.2% respectively. (4) The heat release and combustion efficiency in the combustor will decrease with a decrease in equivalent ratio at the minimal throat height condition where the isolator and the combustor can complete matching operation. This happens when the equivalent ratio and the geometric throat height change synergistically.