Shale gas-produced water (PW), the waste fluid generated during gas production, contains a large number of organic contaminants and high salinity matrix. Previous studies generally focused on the end-of-pipe treatment of the PW and ignored the early collection process. In this study, the transformation of the molecular composition and microbial community structure of the PW in the transportation and storage process (i.e., from the gas-liquid separator to the storage tank) were investigated. As the PW was transported from the gas-liquid separator to the portable storage tank, the dissolved organic matter (DOM) showed greater saturation, less oxidation, and lower polarity. DOMs with high O/C and low H/C ratios (numbers of oxygen and hydrogen divided by numbers of carbon) were eliminated, which may be due to precipitation or adsorption by the solids suspended in the PW. The values of double-bond equivalent (DBE), DBE/C (DBE divided by the number of carbon), and aromatic index (AI) decreased, likely because of the microbial degradation of aromatic compounds. The PW in the gas-liquid separator presented a lower biodiversity than that in the storage tank. The microbial community in the storage tank showed the coexistence of anaerobes and aerobes. Genera related to biocorrosion and souring were detected in the two facilities, thus indicating the necessity of more efficient anticorrosion strategies. This study helps to enhance the understanding of the environmental behavior of PW during shale gas collection and provides a scientific reference for the design and formulation of efficient transportation and storage strategies to prevent and control the environmental risk of shale gas-derived PW.