The mobile ad hoc network (MANET) is a kind of dynamic, easy to construct and universal network, which has been widely concerned by a large number of researchers. Graph theory provides an effective theoretical tool for MANETs modeling and analysis. Clustering is one of the most effective methods to measure network performance with different attributes. This paper gives the basic concept of graph kernel and discusses the principle of optimizing graph kernel and multi-graph kernel. In this paper, we propose a Graph Kernel based Clustering Algorithm in MANETs (GKCA). The GKCA algorithm gives the basic concept of graph kernel, discusses the principle of optimizing graph kernel and multi-graph kernel, and proposes the basic principle based on d-hop graph kernel. GKCA algorithm uses shortest path (SP) to connect different cluster head nodes for packet transmission. The performance of GKCA algorithm, such as the control packets ratio, packets loss ratio, and average end-to-end delay are experimentally evaluated using network simulation (NS2) software. Experimental analysis shows that the proposed approach is efficient, and its performance advantage in dynamic mobile networks is promising.