Under the trend of engine downsizing, limited installation space leads to the intake pipe configuration becoming more complex, and the components, such as the air filter and the intercooler in two-stage compression systems, are much closer to the compressor inlet. The intake pipe configuration becomes essential and nonnegligible for the flow stability of the compression system. Experimental investigations on the flow instability evolution of two compression systems with and without an upstream plenum, which represents the volume influence of the air filter or the intercooler, were carried out in this paper. The results show that there exists a two-regime-surge phenomenon in the compression system without the plenum at the medium- and high-speed lines while this phenomenon disappears in the system with the plenum in which the instability evolution is straightforward. Although the deep surge boundary shifts to the right compared to the system without the plenum, the mild surge boundary shifts to the left, which demonstrates that the pipe configuration with the plenum is beneficial for extending the compressor stable work range. From the perspective of energy input and dissipation, the dissipation ability of the system with the plenum is weaker, so once mild surge occurs, the compression system will fall into deep surge very soon. In contrast, the system without the plenum can stand the oscillations from mild surge much longer before falling into deep surge. These findings shed more light on the flow instability mechanism of compression systems and provide some guidance for the installation and integrated design of compression systems.