In applying word-based dependency parsing such as Universal Dependencies (UD) to Japanese, the uncertainty of word segmentation emerges for defining a word unit of the dependencies. We introduce the following hierarchical word structures to dependency parsing in Japanese: morphological units (a short unit word, SUW) and syntactic units (a long unit word, LUW). An SUW can be used to segment a sentence consistently, while it is too short to represent syntactic construction. An LUW is a unit including functional multiwords and LUW-based analysis facilitates the capturing of syntactic structure and makes parsing results more precise than SUW-based analysis. This paper describes the results of a feasibility study on the ability and the effectiveness of parsing methods based on hierarchical word structure (LUW chunking+parsing) in comparison to single layer word structure (SUW parsing). We also show joint analysis of LUW-chunking and dependency parsing improves the performance of identifying predicate-argument structures, while there is not much difference between overall results of them. not much difference between overall results of them.