Amongst the spaces in which human beings attend, the house is the place where one affects and is affected by it on a daily basis. Each of the various spaces of the house possesses unique characteristics and various factors such as climate, culture, society, and others contribute in the formation of them. The establishment of these spaces at the side of one another gives rise to different spatial systems that lead to the formation of various types in this kind of architecture and influences the shape of the various patterns of using them in addition to bringing about shape differences. The present study aims at investigating and comparing the functional efficiency of the houses in three house patterns with large, small and micro modules using space-related mathematical relations. To do so, nine traditional houses have been selected for the aforementioned three spatial systems in the cities of Kashan, Isfahan, and Yazd as the case studies. The study method in this research is descriptive-analytical and the type of the inference applied herein is deductive of the comparative type. The initial data were extracted through drawing graphs related to the plans of each of the studied houses; then, these data were inserted into the mathematical relations of spatial syntax. This way, based on the indices “spatial value”, “mean depth of the space” and “relative integration”, the functional efficiency of each of the aforementioned patterns was extracted. The results signified that the houses with a large module have the highest spatial value, highest depth amount and highest relative integration rate that altogether eventually result in the increase in the functional efficiency of such a pattern of the house in contrast to the small- and micro-module house patterns. Moreover, the investigation of the spatial difference in the nine studied patterns indicated the existence of similarities in the configuration and spatial organization of the houses in Kashan and Isfahan and their differences from the houses in Yazd in this regard.