The relationship between mixing time and methane production was investigated by anaerobically co-digesting food waste (FW) and chicken manure (CM) at four different organic loading rates. The mixing pattern and turbulence intensity obtained from CFD were adopted to evaluate the mixing performance in digesters with different viscosities. The simulated mixing time from CFD was selected as a reference for the first time to analyze the methane yield. The results showed that if the digester was well mixed under intermittent mixing mode with relatively short mixing time, then extending mixing time or changing intermittent mixing to continuous mixing would have no substantial effects on methane production. By contrast, continuously mixed digesters performed better when the intermittent mixing modes cannot make the digester get to a high degree of uniformity. Hence, the simulated mixing time from CFD can be used as a reference to determine the experimental mixing time in different cases.