<p>The penetration performance of an underwater shaped charge jet (USCJ) under the influence of an intervening water layer was studied by combining experimental and numerical simulation methods, considering the effects of initiation manners and standoff distance. First, the USCJ formation and its penetration performance tests were carried out, which were used to verify the reliability of the numerical simulation. Then, the formation and penetration processes of the shaped charge jet were analyzed experimentally and numerically. The results showed that during the penetration of the intervening water layer, the high-speed and high-energy jet head was engulfed by the water layer. A 30 mm intervening water layer reduces the kinetic energy of USCJ by approximately 13.6% and its penetration performance by 12.8%. The depth of penetration (DOP) of the USCJ decreases with increasing water layer thickness, and its decreasing trend gradually slows down. The DOPs of USCJ under annular and surface initiation manners are greater than those under central initiation. When the annular initiation radius increases, the accumulation effect of the USCJ weakens, and the overall velocity and kinetic energy increase, resulting in a significant increase in DOP. The DOP of USCJ increases initially and then decreases with an increase in the standoff distance; however, an increase in the water layer thickness reduces the optimal standoff distance. While the water layer reduces DOP, it also has a certain effect on the standoff distance. A certain thickness of the water layer is beneficial for the improvement of the DOP when the standoff distance is small.</p>