The invention relates to a heparin alendronate sodium conjugate synthetic method and drugs in the field of medicine. The heparin alendronate sodium conjugate synthetic method comprises the steps: step1, firstly, dissolving 2-chloro-4,6-dimethoxy-1,3,5-triazine in tetrahydrofuran, adding 4-methylmorpholine, stirring for 1-2 h at room temperature, collecting by filtration and washing a precipitatefive times with THF, and thus then obtaining a DMT-MM condensation agent after 48 h of vacuum drying; and step 2, adding heparin and the condensation agent into ultra-pure water, stirring for 1 h, then adding an alendronate sodium solution into the mixed solution of heparin and the condensation agent, carrying out reaction for 24-48 h, pouring the solution into a dialysis bag, dialysing for 48-72h, changing water once every 4 h, finally, freeze-drying the product obtained from dialysis, and thus obtaining the heparin alendronate sodium conjugate drugs. In the method, alendronate sodium is modified by heparin, so the solubility of the drugs is increased, the bioavailability is improved, the cytotoxicity is reduced and the formation of osteoclasts is effectively inhibited.