Downsizing to sub-nm is a general strategy to reduce the cost of catalysts. However, theoretical Wulff-constructed model suggests that sub-nm clusters show little activity for various reactions such as ammonia decomposition and ammonia synthesis because of the lack of active sites. As clusters may deviate from the ideal model construction under reaction conditions, a host–guest strategy to synthesize thermally stable 1.0 nm monodispersed Ru clusters by the pyrolysis of MIL-101 hosts is reported here to verify the hypothesis. For ammonia decomposition, the activity of the Ru clusters is 25 times higher than that of commercial Ru/active carbon (AC) at full-conversion temperature, while for ammonia synthesis, the activity of the Ru clusters is 500 times as high as that of promoted Ru NPs counterpart. The catalyst also maintains its activities for 40 h without any increase in the size. This model can be used to develop a host–guest strategy for designing thermally stable sub-nm clusters to atomic–efficiently catalyze reactions.