Manganese (Mn) is an essential trace element for livestock, but little is known about the optimal Mn source and level for yak. To improve yak's feeding standards, a 48-h in vitro study was designed to examine the effect of supplementary Mn sources including Mn sulfate (MnSO4), Mn chloride (MnCl2), and Mn methionine (Met-Mn) at five Mn levels, namely 35 mg/kg, 40 mg/kg, 50 mg/kg, 60 mg/kg, and 70 mg/kg dry matter (includes Mn in substrates), on yak's rumen fermentation. Results showed that Met-Mn groups showed higher acetate (p < 0.05), propionate, total volatile fatty acids (p < 0.05) levels, ammonia nitrogen concentration (p < 0.05), dry matter digestibility (DMD), and amylase activities (p < 0.05) compared to MnSO4 and MnCl2 groups. DMD (p < 0.05), amylase activities, and trypsin activities (p < 0.05) all increased firstly and then decreased with the increase of Mn level and reached high values at 40-50 mg/kg Mn levels. Cellulase activities showed high values (p < 0.05) at 50-70 mg/kg Mn levels. Microbial protein contents (p < 0.05) and lipase activities of Mn-Met groups were higher than those of MnSO4 and MnCl2 groups at 40-50 mg/kg Mn levels. Therefore, Mn-met was the best Mn source, and 40 to 50 mg/kg was the best Mn level for rumen fermentation of yaks.