In the marine environment, the seabed contains a certain amount of clay. Experimental studies show that the liquefaction susceptibility of the sandy seabed increases as clay content (CC) rises to a certain threshold, beyond which further increases in CC reduce liquefaction susceptibility. However, numerical models that describe the effect of CC on seabed liquefaction are very limited. This study proposed a dynamic poro-elasto-plastic finite element method model for analyzing liquefaction in the sandy seabed with CC below the threshold. Based on a series of undrained triaxial compression tests on sand-clay mixtures from existing literature, a unified constitutive framework was demonstrated to be effective for describing the liquefaction behavior of sand with low CC using one set of model parameters. Existing wave flume model tests validated the effectiveness of the proposed seabed model in describing the effect of low CC on excess pore water pressure (EPWP). Numerical results confirmed that adding a small amount of clay to the seabed increased the soil contraction and thus its liquefaction susceptibility. Wave-induced liquefaction was limited to a certain depth of the seabed, and the liquefaction depth was significantly affected by the CC. Adding a low content of clay the sandy seabed significantly increased both horizontal and vertical displacements under wave action, potentially leading to the instability of the seabed. This study provides a new method for accurately assessing the wave-induced stability of marine structures built on the sandy seabed containing certain amounts of clay.