Anaerobic hydrogen and methane production from cassava stillage in continuously stirred tank reactor (CSTR) were investigated in this study. Results showed that the heat-pretreatment of inoculum did not enhance hydrogen yield compared to raw inoculum under mesophilic condition after continuous operation. However, the hydrogen yield increased from about 14 ml H2/gVS under mesophilic condition to 69.6 ml H2/gVS under thermophilic condition due to the decrease of propionate concentration and inhibition of homoacetogens. Therefore, temperature was demonstrated to be more important than pretreatment of inoculum to enhance the hydrogen production. Under high organic loading rate (OLR) (>10 gVS/(L·d)), the two-phase thermophilic CSTR for hydrogen and methane production was stable with hydrogen and methane yields of 56.6 mlH2/gVS and 249 mlCH4/gVS. The one-phase thermophilic CSTR for methane production failed due to the accumulation of both acetate and propionate, leading to the pH lower than 6. Instead of propionate alone, the accumulations of both acetate and propionate were found to be related to the breakdown of methane reactor.