In the present study, isopropyl alcohol containing wastewater generated from silicon solar cell manufacture was sequentially treated with sequencing batch biofilm reactor and sequencing batch reactor. Sequencing batch biofilm reactor could remove 90 % of isopropyl alcohol from wastewater efficiently as the chemical oxygen demand lower than 1,200 mg L−1. However, 1,600 mg L−1 of chemical oxygen demand damaged the biofilm. The operation mode was changed to sequencing batch reactor on day 30, and sequencing batch reactor showed a greater ability to remove isopropyl alcohol. When the influent chemical oxygen demand was 1,600 mg L−1, the reactors achieved stable removal efficiencies of >95 % for chemical oxygen demand, and the effluent chemical oxygen demand was lower than 100 mg L−1. Denaturing gradient gel electrophoresis analysis showed an increase in bacteria diversity as the operation mode was switched from sequencing batch biofilm reactor to sequencing batch reactor, which might increase the stability of flocs in sequencing batch reactor. Though 13 bands were sequenced from the denaturing gradient gel electrophoresis and a phylogenetic analysis was conducted based on these sequences, it is difficult to analyze the function of these predominant strains in the reactors. Two models were constructed for interpreting the structure of biofilm in sequencing batch biofilm reactor and flocs in sequencing batch reactor, respectively. Higher efficient transfer rate of dissolved oxygen in flocs was proposed as the main reason for the higher isopropyl alcohol removal ability in sequencing batch reactor.