Few models were constructed to depict the influence of land structure change on water and soil resources balance, most of which were based on the simple water balance equation or conceptual model and hardly reflected the influence of uneven spatial distribution and change of water and soil resources on water and soil resources balance. Based on the conception of FH69 blueprint model and LBM, grid LBMGTOPMODEL was constructed. PDSI index of Naolihe River Basin was calculated quantitatively by means of LBMGTOPMODEL and GIS taking grid as a unit, based on data in 1990 without paddy farmland and data in 2013 with paddy farmland. And then the impact of land structure change on water and soil resources balance was assessed according to the PDSI index. Results showed that there was little change of areas of grassland, woodland and building land during 1990—2013. The change of farmland was mainly due to turn of unused land and drought farmland into paddy farmland, but the draught farmland was still the main type of farmland. During rice growth period from May to early August, the increase of evapotranspiration, decrease of water supply, increase of water loss, and increase of suitable rainfall in downstream slope of paddy farmland resulted in the increase of evapotranspiration constant and decrease of water supply constant, and corresponding increase of runoff constant, water loss constant and climate characteristic constant in Naolihe River basin. The frequency of suitable rainfall in paddy was increased obviously, which converted Naolihe River Basin from slight humid region into appropriate farmland, not too wet or too drought. The difference of draught index under two conditions was enlarged at the growth stage of paddy farmland during May and July, while the influence of paddy farmland on draught was decreased as the decrease of water demand of paddy farmland. The results can provide reference for the influence of paddy farmland development on regional water and soil resources balance and regional drought assessment.