Root is essential for anchoring to the land and nutrition uptake in plants. Resolving the trajectories of root cells gives us novel insights into plant adaption to surrounding habitat. The single cell expression analysis has been proved to be powerful tool to study cell heterogeneity. Bread wheat as a hexaploid species contains three sub-genomes, the extremely complex and large genome may generate more complex differentiated trajectories for root cells. But the coordinated mechanisms among the homoeologs from three sub-genomes to regulate the wheat root development remains unclear. Here, we performed a snRNA-seq and snATAC-seq with wheat root tips. We annotated the potential marker genes for each cell cluster and identified commonly seen root cell types in wheat, such as the vascular cells, cortex, endodermis, epidermis and root hair cells. We surveyed the sub-genome asymmetry gene transcription in wheat root in single cell resolution and revealed that the asymmetry pattern of homoeologs are cell type dependent. There are 50%-75% genes in QC cells, columella, root border cells, and companion cells in an unbalanced manner. The asymmetric expression of cells increased along with the differentiated trajectory of vascular tissue. This asymmetric pattern also related with the asymmetry of accessible chromatin. In addition, the constructed cell differentiation trajectories suggested that cortex and endodermis originated from ground meristem and proximal meristem, respectively in wheat root, which differs from the situation in Arabidopsis. We also found that DAR2 and DAA1 may function to promote the differentiation of companion cells and sieve element, respectively. Taken together, applying the nuclei based single cell transcriptome and open chromatin analysis in wheat, we described root organization in wheat and in particular, we demonstrated the sub-genome asymmetry in signle cell level in polyploidy species.