Although many methods of spatial analysis have been developed for a better understanding and modelling of urban space analysis, there is still a need for exploration of new analytical techniques for modelling urban spaces. Space Syntax models the spatial configurations of urban spaces by using a connectivity graph representation. Such a configuration of space identifies patterns that can be used to study urban structures and human behaviors. This paper tries to present a new methodology to investigate the urban spatial structure by using Space Syntax with the GIS information including land use, buildings’ characteristics and practical evaluations of the potential of the Space Syntax approach with GIS and multivariate analysis technique. Finally we try to offer some recommendations that attempt to improve the identified problems faced in Kitakyushu, Japan.