In today’s dynamic business environment, the competition pattern is essentially the competition of one supply chain with another rather than single enterprise. Thus, collaborations in enterprises emerge as the times require. Along with the benefits brought by these kinds of collaborations, the risks arising in the cooperation process produce extra costs as well. Therefore, cost control is extending from the internal microscopic focus to the external interactive processes. The traditional cost control methods have limitations in coping with the new risks resulted from the supply chain. By taking into account the external risks level, this paper constitutes a cost control model based on supply chain operational risks which has improved the Activity-based costing and put forward a new perspective in supply chain cost optimization.