Increment of cultivated lands value is an important way to increase farmers' income and the most effective way to protect cultivated land. A reasonable layout of cultivated land is considered as one of most effective method to raise land value. Domestic and foreign studies, which focus on how to establish cultivated land use layout from variant perspectives, suggested that designing farmland production layout based on integration of natural and economic factors can not only optimize economic and ecological benefits, but also be the most effective way to protect cultivated land. However, there has no practical method to integrate two types of factors at present yet. In this study, taking Pujiang County as an example, natural and economic factors that affect crop growth are refined and integrated as a comprehensive index to build an optimization model for the county cropland layout using the GIS technology. First, the cultivated land of Pujiang county was divided to 9 natural units by overlapping relative natural factors in ArcGIS, such as topography, landform, soil, hydrology, and climate; then 431 economic units were generated based on ecological niche socio-economic value (NSEV), which were further integrated with natural units to construct comprehensive factors unit of crop. Finally, taking account of the local representative crop, such as rice, vegetables and fruits as reference, optimized county cropland layout aimed to obtain maximum suitability and comprehensive benefits was build. According to the designed cultivated land layout, the total area of rice paddy field of Pujiang county is about 6389.57 hm², which is very close to the last three years averaged area of planted rice paddy land of 6758 hm²; the total area of vegetable land is estimated as 2552.87 hm², which is higher than the averaged planted area-3890 hm² (multiple cropping coefficient is 2.0). However, it is coincident with the expectation of development; the total area of orchard land is 2751.80 hm², which is smaller lower than averaged area-2819 hm². Nevertheless orchard land use can be adjusted according to market situation at farmer's will. In general, the results of designed cultivated land layout are consistent with the local practice, indicating practicability and validity of the proposed method. The results also suggest that designing cropland production layout based on comprehensive index by integrating natural factors and NSEV can reduce the arbitrary effect of subjective factors and has pointed strategy in terms of selecting suitable natural and economic factors for local representative crops.