An investigation was conducted on a self-agitation anaerobic baffled reactor (SA-ABR) with agitation caused solely by the release of stored gas. The compound in the reactor is mixed without the use of any mechanical equipment and electricity. The computational fluid dynamics (CFD) simulation used to provide details of the flow pattern and information about the agitation process and a solid basis for design and optimization purposes. Every self-agitation cycle could be separated into the pressure energy storage process, the exergonic process and the buffer stage. The reactor is regarded as the combination of continuous stirred tank reactor and a small plug flow reactor. The liquid level and diffusion varies widely depending on the length of the U-tube. The compound transition phenomenon in the 1st chamber mainly occurs during the energy exergonic process and buffer stage. The fluid-diffusion in the 3rd and 4th chambers mainly happens after the buffer period.