Thermal　hydrolysis　facilitates　anaerobic　digestion　process,　but　raises　the　possibility　of　free　ammonia　inhibition.　This　study　evaluated　the　effect　of　free　ammonia　on　the　methanogenic　ability　of　the　thermal　hydrolysis　and　mesophilic　combined　process　treating　waste　activated　sludge　(WAS)　with　conventional　single　phase　process　as　comparision.　At　the　volumetric　organic　loading　rates　of　1.74~4.27　gVS/(L·d),　the　combined　process　had　89%~121%　methane　production　and　1.21~1.46　times　volatile　solids　reduced　than　the　conventional　process.　But　it　produced　free　ammonia　(FA)　ranging　89~382　mgN/L,　much　higher　than　that　(37~84　mgN/L)　in　the　conventional　process.　Anaerobic　microorganisms　in　both　processes　acclimated　to　high　FA　concentrations.　The　aceticlastic　methanogenesis　pathway　was　barely　affected　in　the　conventional　process　with　FA　increasing　from　43　to　84　mgN/L,　while　the　activity　of　aceticlastic　methanogens　was　inhibited　in　the　combined　process　with　FA　concentration　higher　than　264　mgN/L.　The　interaction　of　FA　concentration,　BMP　utilization　ratio,　the　inhibition　of　aceticlastic　methanogenesis　and　volatile　fatty　acid　(VFA)　accumulations　indicated　the　combined　process　was　mainly　affected　by　nitrogen　loading,　which　was　different　from　organic　loading　limited　conventional　process.　At　high　solid　concentration,　nitrogen　loading　rates　should　be　considered　as　an　limiting　operational　parameter　for　thermal　hydrolysis　anaerobic　digestion　process.　©,　2015,　Chinese　Society　for　Environmental　Sciences.　All　right　reserved.