Nationwide surveys of food and nutrient intake in China have revealed geographical variation between urban and rural areas. This study developed a semi-quantitative food frequency questionnaire (SQFFQ) for cancer risk assessment suitable for both urban and rural populations by conducting a survey of food intake in Chongqing, China. We recruited 100 urban and 104 rural healthy residents aged from 35 to 55 years in Chongqing, and collected dietary data with 3-day weighed records to assist in the development of the SQFFQ. The intake of 35 nutrients was calculated according to Standard Food Composition Tables for China and Japan. For each nutrient estimated by percentage contribution analysis (CA) and multiple regression analysis (MRA), foods with up to a 90% contribution or a 0.90 cumulative R(2) were selected as items for SQFFQs. The food items of the combined SQFFQ were selected from all items listed in either urban or rural SQFFQs. Mean intake of energy, protein and carbohydrate did not differ between the urban and rural residents. The latter consumed more fat than their urban counterparts. We selected 119 food items for the combined SQFFQ, comprising 22 specific items for the urban SQFFQ, 6 for the rural, and 78 common and 13 additional items. The combined SQFFQ covered 33 nutrients with up to a 90% contribution in each area. We were able to develop a data-based SQFFQ that can estimate nutrient intake of both urban and rural populations, with suitable coverage rates. Further reliability and reproducibility tests are now needed to assess its applicability.