The degree-constrained minimum spanning tree (dc-MST) problem is of high practical importance. Up to now there are few effective algorithms to solve this problem because of its NP-hard complexity. More recently, a genetic algorithm (GA) approach for this problem was tried by using Prüfer number to encode a spanning tree. The Prüfer number is a skillful encoding for tree but not efficient enough to deal with the dc-MST problem. In this paper, a new tree-based encoding is developed directly based on the tree structure. We denote it as tree-based permutation encoding and apply it to the dc-MST problem by using the GA approach. Compared with the numerical results and CPU runtimes between two encodings, the new tree-based permutation is effective to deal with the dc-MST problem and even more efficient than the Prüfer number to evolve to the optimal or near-optimal solutions.