Aiming at relieving acid accumulation in anaerobic digestion (AD), syntrophic associations of syntrophic fatty acid-oxidation bacteria and H2/formate-scavenging methanogens were enriched by feeding propionate, butyrate and formate in an up-flow anaerobic sludge blanket (UASB) reactor. Results showed that methane yield increased by 50% with increasing formate concentration (0–2000 mg COD/L). In addition, the abundance and quantity of SFOB (Syntrophobacter, Smithella and Syntrophomonas) and H2/formate-scavenging methanogens (Methanobacteriales and Methanomicrobiales) were increased after microbial acclimation. The enriched syntrophic associations showed higher propionate and butyrate removal efficiencies of 98.48 ± 1.14% and 99.71 ± 0.71%, respectively. Furthermore, encoding genes of formate dehydrogenase and hydrogenases presented higher abundances after microbial enrichment, which suggested that the enhancements of interspecies formate transfer and interspecies hydrogen transfer between syntrophic associations benefited volatile fatty acids (VFAs) conversion. This research provided an effective strategy to relieve acid accumulation.