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The application belongs to the field of treating blood vessel-bone coupling imbalance diseases in traditional Chinese medicine, and particularly relates to a composition for treating blood vessel-bone coupling imbalance diseases, a pharmaceutical preparation and application. Geniposide alone or in combination with crocin I can effectively reduce endothelial cell damage under pathological stimulation conditions, reduce the level of cell apoptosis and the degree of oxidative stress, improve the vascular endothelial function state, and can also significantly inhibit osteoclast differentiation, reduce the number of mature osteoclasts, and reduce bone resorption activity, thereby being conducive to restoring the dynamic balance between bone formation and bone resorption.