The effects of biochar on karstic lime soil physicochemical properties, soil microbial community diversity and plant physiology are poorly understood. To clarify these effects of biochar application, we applied biochar on the soil surface of Sichuan pepper (Zanthoxylum schinifolium) stands. One year later, leaf gas exchange and chemicals as well as soil physicochemical properties and microbial community composition were assessed. Biochar significantly increased photosynthesis, stomatal conductance, transpiration rate and total nitrogen and phosphorus in leaves, but it did not significantly affect total chlorophyll content and malondialdehyde. Total nitrogen and phosphorus as well as available phosphorus and potassium in the soil were significantly increased by biochar. However, soil pH, water content, bulk density, abundance of soil microbes (actinomycetes, bacteria, fungi and Gram negative and positive bacteria), and soil microbial community structure did not exhibit significant increases. Soil total phosphorus, available nitrogen, available phosphorus and available potassium positively correlated with the abundance of soil bacteria, fungi and actinomycetes. These results indicate that biochar enhanced main plant nutrients and improved gas exchange of pepper plants and physicochemical properties of karstic lime soil.