Extrapallial fluid (EPF) is located between the shell and the mantle, and it is believed to play key roles in shell biomineralization in Pinctada fucata. However, few studies have been performed on the biomineralization effect of EPF. In this work, CaCO3 crystallization experiments showed that EPF proteins could not only control the morphology but also regulate the phase transition of calcium carbonate through the different proteins specific binding to calcite or aragonite. In crystal growth inhibition experiments, when the final concentration of CaCl2 and NaHCO3 reduced from 50 to 5 mM, the function of EPF proteins (50 μg/mL) transferred from significantly improving over the number of CaCO3 crystals (448 ± 28) upon the control (128 ± 20) to inhibiting the precipitation of CaCO3. The precipitation rate of CaCO3 was also inhibited by EPF proteins. In vivo, once EPF was extracted daily for 20 days, the nacre platelet in the nacreous layer was disturbed, and calcite deposited randomly due to the reduction of...