Zonal characterstics of nitrogen and phosphorus efficiency of rice landraces were investigated, based on relative index of 16 morphological traits within the core collection of 548 accessions from 16 prefectures in Yunnan Province, using SPSS software analysis and potted plant trials with red soil, and setting four treatments between unapplied phosphorus (available phosphorus 0.02 mg·kg-1) versus applied phosphorus (available phosphorus 69.76mg·kg-1) as well as unapplied nitrogen(available nitrogen 156.7mg·kg-1)and applied nitrogen(available nitrogen 232.18mg·kg-1). Results are as follows: Ecological difference of phosphorus response of morphological traits for rice landraces in Yunnan under phosphorus deficiency stress is more significantly than that of nitrogen response; The relative index of six traits(stem-tiller number, stalk weight, biomass, root weight, total plant weight and spike weight) are gene type screening index for nitrogen and phosphorus efficiency tolerance of core collection for rice landraces in Yunnan, and reflecting its zonal characterstics of nitrogen and phosphorus efficiency. Cluster analysis showed that 16 prefectures are divided into three zonal type based on the nitrogen and phosphorus efficiency characterstics of core collection for rice landraces in Yunnan Province, and it is associated with the cordillera,water system,soil fertility,ecological factors and genetic diversity.