Aim To observe the structural changes of human coronary atherosclerotic lesions and the expression of CD40L and matrix metalloproteinase-9 (MMP-9) protein, and to explore the role of CD40/CD40L signaling in the development of human coronary atherosclerosis. Methods 60 cases of human coronary artery with different degrees of atherosclerosis were collected as experimental group, and 12 cases without pathological changes were as control group. HE staining was used to observe the histological structure of coronary artery in the two groups, and image analysis software was used to detect the related indexes of the lesion structure. The expression levels of CD40L and MMP-9 protein were detected by immunohistochemical staining. The relationship between the expression of CD40L and MMP-9 and the structural changes of atherosclerotic lesions were analyzed. Results The expression of CD40L protein was enhanced in all the atherosclerotic coronary artery, and it was mainly expressed in the foam cells of the plaques shoulder and bottom. Moreover, the expression level of MMP-9 protein in the lesion was increased and it was positively correlated with the CD40L expression and the lesion size especially the necrosis size. There was no correlation between the expression level of MMP-9 and the thickness of fibrous cap. The ratio of fibrous cap thickness to the maximum intimal thickness was decreased with the increase of MMP-9 level. Conclusions The expressions of CD40L and MMP-9 protein are significantly enhanced in the human coronary atherosclerotic lesions. CD40L may promote the expression of MMP-9, to strengthen the extracellular matrix decomposition in vascular lesions, so as to promote the development of lesions and the enlargement of necrotic foci, thus the stability of atherosclerotic lesions is decreased.