Surgical treatment of benign subchondral lesions is the preferred treatment approach, but it leads to bone defects and requires filling treatment. MIIGX3 calcium sulfate bone cement is a new type of bone filling material. However, whether it affects bone defects after scraping benign lesions under the cartilage is unknown. SD rats were used to prepare the cartilage defect model on the femoral block and divided into control group, medical bone cement group and MIIGX3 calcium sulfate bone cement group followed by analysis of bone mineral density, ALP activity, type II collagen and BMP-2 level and TNF-alpha and IL-6 secretion by ELISA, COL2A1 and SOX9 expression by Real time PCR as well as glycosaminoglycan (GAG) content. The medical bone cement and MIIGX3 calcium sulfate bone cement can significantly increase ICRS score, bone density and ALP activity, elevate type II collagen and BMP-2 secretion and the expression of COL2A1 and SOX9 and GAG content compared to control (P < 0.05); MIIGX3 calcium sulfate bone cement can significantly improve these changes (P < 0.05). The TNF-alpha and IL-6 secretion of medical bone cement was increased but decreased in MIIGX3 group (P < 0.05). MIIGX3 calcium sulfate bone cement filled with benign lesions of subchondral bone after scraping can promote chondrocyte differentiation and expression, promote cartilage growth and reduce cartilage defects.