Commuting flow prediction is an essential task for municipal operations in the real world. Previous studies have revealed that it is feasible to estimate the commuting origin-destination (OD) demand within a city using multiple auxiliary data. However, most existing methods are not suitable to deal with a similar task at a large scale, namely within a prefecture or the whole nation, owing to the increased number of geographical units that need to be maintained. In addition, region representation learning is a universal approach for gaining urban knowledge for diverse metropolitan downstream tasks. Although many researchers have developed comprehensive frameworks to describe urban units from multi-source data, they have not clarified the relationship between the selected geographical elements. Furthermore, metropolitan areas naturally preserve ranked structures, like cities and their inclusive districts, which makes elucidating relations between cross-level urban units necessary. Therefore, we develop a heterogeneous graph-based model to generate meaningful region embeddings at multiple spatial resolutions for predicting different types of inter-level OD flows. To demonstrate the effectiveness of the proposed method, extensive experiments were conducted using real-world aggregated mobile phone datasets collected from Shizuoka Prefecture, Japan. The results indicate that our proposed model outperforms existing models in terms of a uniform urban structure. We extend the understanding of predicted results using reasonable explanations to enhance the credibility of the model.