Microarray data analysis is a very popular topic of current studies in bioinformatics. Most of the existing methods are focused on clustering-related approaches. However, the relations of genes cannot be generated by clustering mining. Some studies explored association rule mining on microarray, but there is no concrete framework proposed on three-dimensional gene-sample-time microarray datasets yet. In this paper, we proposed a temporal dependency association rule mining method named 3D-TDAR-Mine for three-dimensional analyzing microarray datasets. The mined rules can represent the regulated-relations between genes. Through experimental evaluation, our proposed method can discover the meaningful temporal dependent association rules that are really useful for biologists.