Co-digestion of food waste and dairy manure in a two-phase digestion system was conducted in laboratory scale. Four influents of R0, R1, R2, and R3 were tested, which were made by mixing food waste with dairy manure at different ratios of 0:1, 1:1, 3:1, and 6:1, respectively. For each influent, three runs of experiments were performed with the same overall hydraulic retention time (HRT) of 13 days but different HRT for acidification (1, 2, and 3 days) and methanogenesis (12, 11, and 10 days) in two-phase digesters. The results showed that the gas production rate (GPR) of co-digestion of food waste with dairy manure was enhanced by 0.8-5.5 times as compared to the digestion with dairy manure alone. Appropriate HRT for acidification was mainly determined by the biodegradability of the substrate digested. Three-, 2-, and 1-day HRT for acidification were found to be optimal for the digestion of R0, R1, and R2/R3, respectively, when overall HRT of 13 days was used. The highest GPR of 3.97 L/L.day was achieved for R3(6:1) in Run 1 (1 + 12 days), therefore, the mixing ratio of 6:1 and HRT of 1 day for acidification were considered to be the optimal ones and thus recommended for co-digestion of food waste and dairy manure. There were close correlations between degradation of organic matters and GPR. The highest VS removal rate was achieved at the same HRT for acidification and mixing ratio of food waste and dairy manure as GPR in the co-digestion. The two-phase digestion system showed good stability, which was mainly attributed to the strong buffering capacity with two-phase system and the high alkalinity from dairy manure when co-digested with food waste.