A pot experiment was conducted to study the bio-environmental effects of lime and organic manure application on red soil and paddy soil derived from red sandstone and polluted by multi-heavy metals. The results indicated that liming decreased the content of soil bioavailable Cu and Pb extracted with 0.05 mol/L HCl, while applying hog manure increased that of Cd. Soil bioavailable heavy metals (HMs) showed an apparent relationship with soil dissolved carbon. Applying lime and organic manure has a positive physiological effect on soil microorganisms and sweet potato. Many indexes, i.e. the number of soil actinomycetes, the content of HMs in the root of sweet potato, showed the remarkable relationship with soil bioavailable Cu, Cd and Pb. However, some indexes of soil and plant only relative to one or two soil bioavailable HMs. For example, soil microbial biomass carbon correspondent with soil bioavailable Cd. Only the content of Cu in the stem and leaf showed a notable relationship with soil effective Cu. Soil effect Cu and Pb rather Cd showed remarkable relation with mean transpiration rate, total biomass and leaf area index of sweet potato. The daily mean value in the seedling stage showed a stronger relationship with soil bioavailable Cu and Pb. Therefore these two physiological indexes can reflect the change of soil metallic contamination.