In order to solve the problem of pollution of acid mine drainage (AMD), such as low pH value and being rich in SO42−, Fe and Mn pollution ions, etc., immobilized particles were prepared by using sugar cane-refining waste (bagasse), a natural composite mineral (called medical stone in China) and sulfate-reducing bacteria (SRB) as substrate materials, based on microbial immobilization technology. Medical stone is a kind of composite mineral with absorbability, non-toxicity and biological activity. The adsorption capacity of medical stone is different according to its geographic origins. Two dynamic columns were constructed with Column 1 filled by Fuxin’s medical stone-enhanced SRB immobilized particles, and Column 2 filled by Dengfeng’s medical stone-enhanced SRB immobilized particles as fillers. The treatment effect on AMD with SRB-immobilized particles enhanced by medical stone from different areas was compared. Results showed that Column 2 had better treatment effect on AMD. The average effluent pH value of Column 2 was 6.98, the average oxidation reduction potential (ORP) value was −70.17 mV, the average removal percentages of SO42−, Fe2+ and Mn2+ were 70.13%, 83.82% and 59.43%, respectively, and the average chemical oxygen demand (COD) emission was 555.48 mg/L.