[Objective] The author aimed to explore the microbial diversity and quality variations of Pu-erh tea at different processing stages (manufacturing, fermentation, and storage). [Method] The microorganisms isolated from tea were cultured and molecularly identified by using plate coating and PCR sequencing technologies. The quality of Pu-erh tea was determined by sensory evaluation, component detection, and electronic nose. [Result] A total of 218 strains of bacteria were isolated and purified, with 77, 59, and 82 strains isolated from sun-dried raw tea (SQ) at the manufacturing stage, fermented ripened Pu-erh tea (SC1) during the fermentation stage, and cellar-aged ripened Pu-erh tea stored for 2 years (SC2) during the storage stage, respectively, and no fungi were isolated. The 16S rRNA gene sequencing revealed that the bacteria mainly classified as Achromobacter, Bacillus, Bacterium, Brachybacterium, Brevibacillus, Chryseobacterium, Staphylococcus, Curtobacterium, Raoultella, Enterobacter, Pantoea, Herbaspirillum, Paenibacillus, Kocuria, Siccibacter, and Xanthomonas. Bacillus was the common dominant bacterium in SQ, SC1, and SC2, with relative isolation frequencies (RDF) of 35.06%, 55.93%, and 36.59%, respectively when incubated at 37 ℃. In addition to Bacillus, the main bacteria in SQ were Chryseobacterium (19.48%), Achromobacter (12.99%), and Curtobacterium (6.49%). The main bacteria in SC1 were Streptomyces (11.86%), Curtobacterium 10.17%), and Kocuria (10.17%). The main bacteria in SC2 were Paenibacillus (15.85%), Enterobacter (12.20%), and Staphylococcus (10.98%). The levels of heavy metals, agricultural residues, pathogenic bacteria, powder, total ash content, crude fiber, tea polyphenol, and water extract of Pu-erh tea all complied with national standards. The mass fractions of total free amino acids, thearubigins, theabrownins, and fluoride, as well as the mass fraction of catechins and other tea polyphenols, were higher than those in SC2, while the mass fractions of caffeine and tea polysaccharides in SC2 were higher than those in SC1. The mass fractions of caffeine and theabrownin in SC1 and SC2 were higher than those in SQ, while the mass fractions of total free amino acid, theanine, thearubigins, and theaflavin as well as the mass fraction of catechins and other tea polyphenols, were all lower than those in SQ. Aroma substances were mainly concentrated in methyl groups, p-sulfide, hydrocarbons, alcohols, aldehydes, ketones, aromatic components, organic sulfide, and benzene. [Conclusion] This study provides a theoretical basis for the development and promotion of the Pu-erh tea industry.