Low-dimensional materials have attracted significant attentions over the past decade. To discover new low-dimensional materials, high-throughout screening methods have been applied in different materials databases. For this purpose, the reliability of dimensionality identification is therefore highly important. In this work, we find that the existence of self-penetrating nets may lead to incorrect results by previous methods. In stead of this, we use the quotient graph to analysis the topologies of structures and compute their dimensionalities. Based on the quotient graph, we can calculate not only the dimensionality but also the multiplicity of self-penetrating structures. As a demonstration, we screened the Crystallography Open Database using our method and found hundreds of structures with different dimensionalities and high multiplicities up to eleven.