Shifang, located in Sichuan Province, is known as the hometown of the Chinese cigar. In Shifang, cigar leaf has been cultivated for nearly 400 years. However, microbial community diversity is poorly understood in the agricultural processing of cigar leaves from Shifang. In this study, based on 16S rRNA and internal transcribed spacer region (ITS) gene Illumina Miseq high-through sequencing, characterization and functional prediction of the microbial community in freshly harvested, air-cured and agricultural fermented cigar leaves were revealed. Results showed that the differences of microbes in periods during agricultural processing were greater than those among varieties. The microbial richness of freshly harvested cigar leaves was the lowest, and microbial diversity of air-cured tobacco leaves was the highest. The richness and diversities of bacterial communities, and numbers of bacterial functional genes in all samples were higher than those of fungal. The dominant microbes belonged to 16 genera, including unclassified_Enterobacteriaceae, Pseudomonas, Chloroplast, Acinetobacter, Pantoea, Sphingomonas, Staphylococcus, Aquabacterium, unclassified_Burkholderiaceae, Methylobacterium, Caulobacter, Brevundimonas, Aspergillus, Alternaria, Sampaiozyma, and Plectosphaerella, of the Proteobacteria, Cyanobacteria, Firmicutes, Basidiomycota, and Ascomycota. Unclassified_Enterobacteriaceae, Alternaria, and Mycosphaerella were significantly positively correlated with freshly harvested cigar leaf group, while unclassified_Burkholderiaceae, Novosphingobium, Pectobacterium, and Aspergillus were significantly negatively correlated with it. Pectobacterium and Aspergillus were significantly positively correlated with agricultural fermented cigar leaf group, while Alternaria, Penicillium, Mycosphaerella, Moesziomyces, Filobasidium, and Nigrospora were significantly negatively correlated with it. The functions of bacteria and fungi were associated with fatty acid/lipid, amino acid, and carbohydrate biosynthesis, and fermentation. Compared to freshly harvested cigar leaves, air-cured and agricultural fermented cigar leaves were more functionally active regarding fatty acid/lipid biosynthesis and aromatic compound degradation from bacteria, and amino acid degradation from fungi. Results in this study advances our understanding of cigar leaf microbiota and their functions, and is of great importance for the production and quality improvement of Chinese cigar leaf.