Phenol, as a very toxic pollutant, exists widely in rivers in China. To explore the effect of bacterial augmentation on phytoremediation of phenol by Acorus calamus L., some plant growth and physiological parameters and percent removal of phenol were determined in hydroponics containing phenol with addition of Bacillus thuringiensis A1. The A. calamus L. and B. thuringiensis A1 consortium increased the growth rate of plant height, chlorophyll content, the activity of superoxide dismutase (SOD) and peroxidase (POD) in A. calamus L. 10.00–36.54%, 0.62 − 22.15%, 3.94 − 11.25% and 1.37–10.50% respectively compared with single plant treatments at same phenol concentrations. However, the addition of B. thuringiensis A1 decreased the content of malondialdehyde (MDA) and relative electrical conductivity (REC) in A. calamus L. 12.99–23.66% and 8.38–29.98% respectively compared with single plant treatments. The removal efficiency of phenol (increased from 1.56% to 13.78%) by the A. calamus L. and B. thuringiensis A1 consortium was higher than the removal efficiency of phenol of the independent A. calamus L. system. In conclusion, the addition of B. thuringiensis A1 alleviated phenol stress to A. calamus L and enhanced phenol removal due to phenol removal by bacterial augmentation. Novelty statement The addition of B. thuringiensis A1 alleviated phenol stress to A. calamus L. and enhanced phenol removal due to phenol removal by bacterial augmentation.