Compared with traditional underwater equipment powered by propeller, the manta-ray-inspired vehicle with MPF mode (Median fin/paired fin) has the advantages of stable swimming attitude, high maneuverability, and low noise, etc. As one of the sources of advancing power when the manta-ray-inspired vehicle swims, the flexible deformation of the pectoral fin is an important factor affecting the hydrodynamic performance. In this paper, a mechanical analysis of the two-dimensional flexible pectoral fin using thin wing theory shows that the main factor affecting the hydrodynamic force of the two-dimensional flexible pectoral fin is the level of curvature of the pectoral fin chordal section. By designing a two-stage bionic skeleton at the leading and rear edges of the manta-ray-inspired vehicle, the root–tip section width of the bionic skeleton is used to characterize the level of the bionic pectoral fin’s flexibility, and a tensiometer is used to quantitatively measure the level of flexibility. The root-to-tip ratio of the cross-section was varied to obtain different levels of pectoral fin flexibility, and the hydrodynamic properties of the pectoral fins during flapping were measured using a force sensor and normalized for analysis. The experimental results show that the reduction of the flexibility of the leading edge and the increase of the flexibility of the rear edge are beneficial to the improvement of the thrust performance, and the experimental results are the same as the distribution of the skeletal flexibility in real organisms. Fitting curves of the pectoral fins’ relative flexibility and the normalized thrust/lift show that the flexibility of the pectoral fins has a significant effect on its hydrodynamic force, and a stiffer leading edge and a softer rear edge can improve the hydrodynamic characteristics of the manta-ray-inspired vehicle. Phase differences interacting with flexibility can also enhance bionic pectoral fins’ dynamic properties within 10~30 degree.