The influence of rarefaction wave on the experimental section in blast shock tube with different isolator lengths was simulated. To simulate the incident wave at the entrance of experimental section exactly and efficiently, a new method which couples 1D and 3D computational programs was adopted, and small scale explosion was utilized to simulate actual overpressure waveforms in 1D computation according to blast similarity rule. The computation results demonstrate the following features: alteration of isolator length L does not affect the peak overpressure; when L is less than or equal to 20m, influence of rarefaction wave will reduce the impact time and impulse of overpressure in experimental section; while L is larger than or equal to 30m, the rarefaction wave doesn't affect these two parameters in experimental section.