Local scour induced by strong currents has become one of the major challenges for sea-crossing bridges built for the convenience of transportation across bays. To mitigate the local scour of the sea-crossing bridge foundation, this study optimized the design and geometry of the upper part of the skirted caisson and proposed a new type of foundation called the skirted caisson with two tandem piers (SCTTP). Systematic experimental and numerical investigations into the influence of the design parameters of SCTTPs on scour protection were conducted, and the temporal development and mechanism of local scour in SCTTPs were investigated. The following conclusions can be drawn: (1) although the scour of the SCTTP is slightly greater than that of the skirted caisson, the scour terrain of the SCTTP is more stable; (2) the scour of the SCTTP with circular piers is small, and the flat surfaces of semicircular-ended and square piers can intensify the scour; (3) the scour at the front and back of the SCTTP gradually becomes independent of the distance between the two piers, causing the total scour of the SCTTP to increase; and (4) as the width of the tie beam decreases, the scour of the SCTTP with the groove becomes more significant than that of the SCTTP with no groove, but the groove depth has little effect on the maximum scour depth of the SCTTP with the groove. These findings provide insight into the design optimization of SCTTPs from scour.