Naturally occurring pearl and its derivatives have recently gained interest in bone regeneration due to their bioactive characteristics and good mechanical properties. In this study, three-dimensional scaffolds composed of poly-l-lactide (PLLA)/aragonite pearl powder, PLLA/vaterite pearl powder and PLLA/nacre powder were fabricated by freeze-drying. Scanning electron microscope (SEM) images indicated that the addition of powder made no visible difference to the morphology of the composite scaffolds. These composite scaffolds were found to have nearly twice the compressive strength and compressive modulus of the pure PLLA scaffold. X-ray diffraction patterns reveal that both PLLA/aragonite and PLLA/nacre composite scaffolds have pure aragonite crystals as their inorganic component, while PLLA/vaterite has pure vaterite crystals. The attachment and morphology of rat bone marrow-derived mesenchymal stem cells (rBMSCs) on scaffolds was observed by the SEM. The proliferation and osteogenic differentiation of rBMSCs on composite scaffolds was also investigated. The results indicate that PLLA/aragonite and PLLA/nacre scaffolds better stimulate cell proliferation and alkaline phosphatase activity than the PLLA scaffold. However, the PLLA/vaterite scaffold appears to decrease rBMSCs proliferation as well as the osteogenic differentiation, possibly due to the high pH of the solution containing PLLA/vaterite.