A conventional anaerobic baffled reactors (ABRs) treating high strength sweet potato starch wastewater at ambient temperatures resulted in acidification and bad performances. After modification, the acidification was remitted and COD removal efficiencies reached 92.73% at high temperatures and were maintained at 71.19% at low temperatures. Moreover, as much as 1.014 ± 0.056 L CH4/L/d were collected at Stage III. The q-PCR results revealed that the largest methanogen populations emerged at Stage III as well, which was 5.29 × 108 mcrA copies per milliliter sludge. A comparable shift in the archaeal community structure at different stages and acetoclastic methanogens Methanosaeta predominated the archaeal community in every compartment in Stages I (63.73%) and II (48.63%). Finally, the net energy gains analysis at mesophilic, thermophilic, and ambient temperature revealed that modified ABR at ambient temperature was not only economical but also profitable and could generated 3.68 KJ energy per gram COD removed.