According to the theory of unintended energy release in accidents, the root cause of a large number of production failures and accidents is usually related to abnormal energy transfer activities during the operation of the manufacturing system. Therefore, from the perspective of inherent safety assurance, a novel mission reliability modeling method that integrates energy activities is proposed. First, the dynamic interaction relationships of production factors are analyzed from the perspective of energy activities, and the connotation of the mission reliability of manufacturing systems oriented to inherent safety are expounded. Moreover, an assessment model for mission reliability of manufacturing systems considering energy activities is analyzed and constructed in terms of self-stabilization capability, anti-disruption capability, and risk-isolation capability. Finally, an industrial case study based on electrochemical ammonia synthesis production system is provided to verify the effectiveness of the proposed method.