Abstract: Empirical studies have demonstrated the positive effects of organic management on farmland biodiversity, but the consistency of this effect between different agricultural habitat types has not been explored. Therefore, a comparison study was conducted between two adjacent farmlands, both with multiple habitats but subjected to contrasting management measures (organic vs. conventional). We sampled spiders using pitfall traps and examined differences in their diversity across organically and conventionally managed farmlands for five different habitat types (vegetable greenhouses, orchards, open-air fields, field margins, and paddy ridges). We also examined how the soil factors affect spider diversity. No significant differences were detected in species richness between the organically and conventionally managed farmlands, but spider abundance in the organically managed orchards was 139% higher than in the conventionally managed orchards. Within the same management system, spider abundance and species richness in the field margins of conventionally managed agricultural areas were 104% and 59% higher than in other habitats, respectively. The difference in spider community composition in organically managed farmland was slightly larger than in conventionally managed farmlands. Meanwhile, the difference in spider community composition between different habitat types was greater in organically managed farmlands than in conventionally managed farmlands. The organic matter content, total nitrogen, and total phosphorus in the soil significantly affected the spider community structure, but these factors did not correlate with spider abundance or species richness. There was a significant negative correlation between total copper (Cu) and spider abundance. This study showed that the spider community is affected by many factors. The management intensity of different habitat types and the vegetation structure were more important than management practices and soil factors. Thus, it is important to create different agricultural habitats and develop organic management techniques to sustain beta-diversity at the landscape scale. Maintaining semi-natural habitats (such as field margins with rich vegetation), reducing agrochemical inputs and disturbances on farmlands, and preventing soil heavy metal pollution may help sustain spider diversity in conventionally managed farmlands.