Barnea manilensis is a bivalve which bores soft rocks, such as, limestone or mudstone in the low intertidal zone. They make burrows which have narrow entrances and wide interiors and live in these burrows for a lifetime. In this study, the morphology and the microstructure of the valve of rock-boring clam B. manilensis were observed using a stereoscopic microscope and FE-SEM, respectively. The chemical composition of specific part of the valve was assessed by energy dispersive X-ray spectroscopy (EDS) analysis. 3D modeling and structural dynamic analysis were used to simulate the boring behavior of B. manilensis. Microscopy results showed that the valve was asymmetric with plow-like spikes which were located on the anterior surface of the valve and were distributed in a specific direction. The anterior parts of the valve were thicker than the posterior parts. EDS results indicated that the valve mainly consisted of calcium carbonate, while metal elements, such as, Al, Si, Mn, Fe, and Mg were detected on the outer surface of the anterior spikes. It was assumed that the metal elements increased the strength of the valve, thus helping the B. manilensis to bore sediment. The simulation showed that spikes located on the anterior part of the valve received a load at all angles. It was suggested that the anterior part of the shell received the load while drilling rocks. The boring mechanism using the amorphous valve of B. manilensis is expected to be used as basic data to devise an efficient drilling mechanism.