Tunnel water leakage is a common issue. Embedded rubber waterstops are crucial in ensuring the waterproofing performance of mountain tunnels. The deformation performance of a rubber waterstop directly impacts its effectiveness, with structural parameters playing a key role. This study employs numerical simulation methods to quantitatively assess the impact of structural parameters-such as the central hole, ribs, and flanges-on the deformation performance of waterstops. The parametric analysis reveals significant variations in how different structural components affect the deformation performance, as indicated by the defined deformation stress influence rate. Specifically, the deformation performance of the embedded waterstop under tensile, compression, and settlement deformations shows a correlation with factors such as the ratio of the central hole opening rate to thickness and the inner and outer diameters. Additionally, an optimization analysis, taking both economic and performance factors into account, was conducted on 16 types of waterstops with different central hole parameters, from which the optimal waterstop was selected. This research provides a scientific basis for enhancing the deformation performance of waterstops and optimizing their structure.