This paper proposes a general framework for structure-preserving model reduction of a second-order network system based on graph clustering. In this approach, vertex dynamics are captured by the transfer functions from inputs to individual states, and the dissimilarities of vertices are quantified by the H-2-norms of the transfer function discrepancies. A greedy hierarchical clustering algorithm is proposed to place those vertices with similar dynamics into same clusters. Then, the reduced-order model is generated by the Petrov-Galerkin method, where the projection is formed by the characteristic matrix of the resulting network clustering. It is shown that the simplified system preserves an interconnection structure, i.e., it can be again interpreted as a second-order system evolving over a reduced graph. Furthermore, this paper generalizes the definition of network controllability Gramian to second-order network systems. Based on it, we develop an efficient method to compute H-2-norms and derive the approximation error between the full-order and reduced-order models. Finally, the approach is illustrated by the example of a small-world network.