To investigate the ossificational process of intermuscular bones in Cyprinus carpio haematopterus, the modified bone clearing and staining experiment were conducted to study the number, morphology, distribution of intermuscular bones in C.c.haematopterus. It was reveled that the initial intermuscular bones were ossified at 14 dpf (day post fertilization) with the standard length of 11.29 mm, in which period the other types of bones had already showed up completely. The first appeared intermuscular bones were located in the tail region and then turned toward the head. When the larvae were 40 dpf with the standard length of 15.60 mm, all the intermuscular bones basically appeared and were equally distributed from the tail to the head. The number of intermuscular bones in C.c.haematopterus ranged from 93 to 104 with an average of 98. The average number of epineurals in each side of the body was 34, and the epipleurals was 15. Seven types were included: non-forked, one-end-unequal-bi-fork, one-end-equal-bi-fork, one-end-multi-fork, two-end-bi-fork, two-end-multi-fork, and tree-branch types. Generally,the morphological complexity of most intermuscular bones in anterior body was greater than that in posterior body. These results will be helpful for us to further understand the molecular mechanism underlying intermuscular bone development as well as the breeding of C.c.haematopterus with fewer or even no intermuscular bone.