The effect of organic materials on the availability of nutrient elements in karst calcareous soil was investigated by a 40-day soil incubation experiment. Biochar, chicken manure and sheep manure were incorporated separately with 1%, 3%, and 5% amount for comparing their impact on soil available N, Fe, and Zn. Our results indicated that chicken manure and sheep manure amendment decreased soil pH, while the opposite was true for biochar. Soil organic matter was enhanced by addition of these organic materials with the order:biochar > chicken manure > sheep manure, but the chemical and microbial activity of organic matter in soil ascribed to biochar application was the lowest. Due to pH, organic matter activity, C/N ratio, and other factors, there was no significant difference between the increment of available N in soil by chicken manure and sheep manure addition with the same amount. Whereas, 5% biochar amendment reduced soil available N significantly. The increment of available Fe and available Zn in soil was optimum by the application of chicken manure, followed by sheep manure and biochar. With 5% addition amount, the contents of available N, available Fe, and available Zn in the soil with biochar were 0.92, 1.13 and 1.21 times as much as that in control respectively, 1.22, 1.63 and 3.39 times respectively for chicken manure treatment, and 1.27, 1.34 and 2.59 times respectively for sheep manure treatment. Hence, compared with biochar, the additions of organic manure were a better choice for the improvement of calcareous soil in karst areas.