Concentrations of 29 elements were analyzed in the marginal area and central area of the shell nacreous layer of the winged pearl oyster Pteria penguin using a laser ablation inductively coupled plasma mass spectrometer. Color of the two shell areas was determined using the color parameter values of lightness, greenness/redness, and blueness/yellowness. It is shown that the concentrations of the elements and the nacreous color are different in the marginal area and central area. The concentrations of Mg, P, B, Li, Cu, and Mo are significantly correlated with lightness and differently distributed in the two shell areas (P < 0.05). The concentration of Na and Mg is significantly related to greenness/redness and differently distributed in the two shell areas (P < 0.05). The concentration of Na, Mg, P, B, Li, and Mo is significantly related to blueness/yellowness and differently distributed in the two shell areas (P < 0.05). The concentration of Mg significantly related to lightness, greenness/redness, and blueness/ yellowness and differently distributed in the two shell areas (P < 0.05). This study provides a new perspective to illustrate the mechanism of color change between the marginal and central areas.