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Integrated partial denitrification-anammox (PD/A) process was considered as a novel strategy for low ammonia wastewater treatment, but the potential roles of the functional bacteria were still unclear. In this study, metagenomic binning analysis coupling with metatranscriptomic analysis was used to reveal the metabolic patterns in a stable operating PD/A system driven by glycerol. The cross-feeding between Bacillusand Candidatus Brocadia, the two dominant functional bacteria that contributed 81.1 % of the total gene expression, was constructed. Bacillusexhibited high nitrite production potential in the assimilatory nitrate reduction pathway instead of partial denitrification. And Bacilluswas the main glycerol utilizer capable of synthesizing intracellular glycogen and polyhydroxybutyrate, which was also the potential branched-chain amino acids and B-vitamins supplier. Candidatus Brocadiaas an anammox bacteria surprisingly expressed the activity of 3-phosphate glycerol (obtained from Bacillus) degradation. This study provided a new understanding of the metabolic patterns and interactions in PD/A system.