Aiming at the problem of various equipment and complicated correlations in operation system-of-systems under the information conditions, an effectiveness evaluation method of system-of-systems based on the operation loop and improved information entropy is proposed according to the traction of enemy targets. The equipment and correlations are abstracted as nodes and edges. The edges’ metrics are determined according to the tactical and technical indexes of the nodes, and the network model of operation system-of-systems based on the operation loop is constructed. The methods to determine the number of the operation loop based on the adjacency matrix and evaluate the effectiveness of the operation loop based on improved information entropy are respectively proposed. The effectiveness evaluation model of operation system-of-systems is built according to the number and effectiveness of the operation loop involved in each target node. Taking an combating large surface warship operation system-of-systems as an example, the results show that the proposed method has fully taken the heterogeneity and uncertainty of each equipment and correlation into consideration to evaluate the effectiveness of the system-of-systems comprehensively and objectively. The proposed method can provide methodological support for the effectiveness evaluation and structural optimization of operation system-of-systems.