The objective of this study was to investigate the effects of long-duration space flight on the biological characteristics of Acinetobacter schindleri (A. schindleri). In this study, an A. schindleri strain was collected from condensate water of the Shenzhou-10 spacecraft and then was sent into space again to the Tiangong-2 space lab for a long-duration spaceflight (64 days). Later, the impacts of the long-duration spaceflight on phenotype, genome and transcriptome of A. schindleri were analyzed. It was found that the long-duration spaceflight markedly decreased the growth rate and biofilm formation ability of A. schindleri. Furthermore, comparative genomic and transcriptomic analyses revealed that the decreased growth rate might be associated with differentially expressed genes (DEGs) involved in transmembrane transport, energy production and conversion, and biofilm was reduced due to downregulation of the pil and algR genes. The findings are of major importance for predicting bacterial pathogenesis mechanisms and possible spacecraft contamination during long-duration spaceflights in the future.