The isomorphism problem involves judging whether two graphs are topologically the same and producing structure-preserving isomorphism mapping. It is widely used in various areas. Diverse algorithms have been proposed to solve this problem in polynomial time, with the help of quantum walks. Some of these algorithms, however, fail to find the isomorphism mapping. Moreover, most algorithms have very limited performance on regular graphs which are generally difficult to deal with due to their symmetry. We propose IsoMarking to discover an isomorphism mapping effectively, based on the quantum walk which is sensitive to topological structures. Firstly, IsoMarking marks vertices so that it can reduce the harmful influence of symmetry. Secondly, IsoMarking can ascertain whether the current candidate bijection is consistent with existing bijections and eventually obtains qualified mapping. Thirdly, our experiments on 1585 pairs of graphs demonstrate that our algorithm performs significantly better on both ordinary graphs and regular graphs.