In this study, a newly established bench-scale thermophilic continuously stirred fluidized bed reactor (CSFBR) was applied for anaerobic co-digestion of food waste (FW) with grease trap waste (GTW). The performance of CSFBR regarding stability and treatment efficiency was inspected through a laboratory contrast experiment with two traditional continuous stirred tank reactors (CSTRs). In the OLR range of 3.19–7.41 g COD/L/d, the methane production rate of the thermophilic CSFBR was about as high as that of the thermophilic CSTR. Nevertheless, the thermophilic CSFBR had much lower VFAs (<1000 mg/L) and LCFA concentrations (<100 mg/L) as compared with the thermophilic CSTR. Unlike the mesophilic CSTR, there was no foaming that occurred in the CSFBR during the whole experimental period. The results all suggested that CSFBR simultaneously provided high treatment capacity and process stability in anaerobic digestion with high-lipid loading.