•UASB performances and microbial mechanisms under pH stress were investigated.•Methane yield was reduced by 25.3% under acidic pH of 5.0.•Primary bacterial communities caused propionate accumulation was found.•Desulfovibrio was dominant syntrophic acetogens.•Methanosaeta was dominant acetotrophic methanogens. The operation performance and microbial mechanisms by pH stress were investigated during anaerobic digestion of sugar refinery wastewater in a upflow anaerobic sludge blanket (UASB) reactor to clarify correlations between pH stress, microbial community and process efficiency. Results showed that the COD removal and methane yield were respectively reduced by 24.8% and 25.3% as pH decreased to 5.0. pH decrease resulted in the composition of dominant fermentative acidogenic bacteria was changed to Butyricicoccus, Lactococcus, Brooklawnia, Armatimonadetes_gp2 and Megasphaera from Prevotella, Streptococcus, Acidaminococcus and Megasphaera, causing an increase in propionate production. In addition, the growth of propionate-oxidizing bacteria was also inhibited at pH 5.0, leading the propionate was accumulated, and then reduced the process efficiency. Methane was mainly produced through acetate cleavage by Methanosaeta during the whole operational period of UASB. pH decrease blocked the metabolic balance and community structure between different trophic groups, resulting in the decrease in reactor performance.