To solve the problems of high concentrations of Cr, SO and H in agate dyeing industrial wastewater and heavy pollution and high treating cost, single-factor and orthogonal experiments were conducted to determine the optimum particle size, the ratio of adsorbents dosing and hydraulic retention time based on peanut shells and scrap iron. Experiments, using five dynamic columns filled with the peanut shells, scrap iron and sulfate-reducing bacteria (SRB), were also conducted to determine the effect and mechanism of treating the wastewater. The results show that the best treatment effect was obtained when the diameter of peanut shells was 3 mesh, scrap iron being 60 mesh size, scrap iron and peanut shells with a ratio of 1:2, and hydraulic retention time being 24 h. By the comprehensive comparison of five groups of columns, the treating effect of column 4 was best, in which the removal rate of SO and Cr was 30.17% and 88.36% respectively before adding the microorganisms, and 25.34% and 99.31% respectively after adding the microorganisms. The average of chemical oxygen demand (COD) release quantity was 62.11 and 513.75 mg·L, and the average effluent pH was 7.09 and 7.93 before and after addition of microorganisms respectively. In conclusion, peanut shells, scrap iron and SRB had a certain synergistic effect on treating agate dyeing wastewater.