The sugar manufacturing industry of Taiwan during the Japanese colonial period changed significantly from the traditional manufacturing process powered by ox carts and stone mills to the use of sugar compression machines. Previous research on factory planning of new sugar factories has focused mainly on location, such as for transportation, raw materials, labor, and so forth. However, few of these studies have mentioned the influence of the prevailing wind. Prevailing winds are an important factor for companies building factories. If factories had not been built on the windward side of the prevailing wind, workers would have suffered from stink and air pollution. The present study reveals the relation between the prevailing wind field and factory planning during the Japanese colonial period. The methodology of this study is based on the analytical method of climatology and objective analysis. The results of the study produced two major findings. (1) Through a comparative analysis of the sugar factories and a timeline of the years in which they were constructed, it was found that the residents in the sugar factory’s residential area suffered a higher risk from stink and air pollution in the early period. However, compared with the earlier period, these risks were lower in the later period. The results showed that the sugar companies have acquired experience after establishing some factories and thus consider the prevailing wind as a major factor in factory planning. Considering the local prevailing winds during the manufacturing season, company houses were built on the leeward side of the entire factory field to avoid pollution from the sugar factories. (2) Different sugar companies had different attitudes toward considering the prevailing wind in factory planning. The sugar factory plans of the Taiwan Seito Kaisha and Meiji Seito Kaisha companies considered the local prevailing winds, except for their first sugar factory in Taiwan. On the other hand, the local prevailing winds were ignored by the two other companies studied in the present work. This demonstrates that there are still some differences regarding consideration of prevailing winds among these sugar companies.