We demonstrate the suppression of soft X-ray high harmonics generated by two-color laser pulses interacting with Ne gas in a gas cell. We show that harmonic suppression can occur at the proper combination of the propagation distance and gas pressure. The physical mechanism behind is the phase mismatch between “short”-trajectory harmonics generated at the early and later times through the interplay of geometric phase, dispersion, and plasma effects. In addition, we demonstrate that the position and depth of harmonic suppression can be tuned by increasing the gas pressure. Furthermore, the suppression can be extended to other laser focusing configurations by properly scaling macroscopic parameters. Our investigation reveals a simple and novel experimental scheme purely relying on the phase mismatch for selectively controlling soft X-ray tabletop light sources without adopting the filters for applications.