Base on the regional climatic characteristics,the clear flavor type of Yunnan tobaccos is divided into 4 subtypes,and the subtype II of clear flavor tobaccos producing areas are mainly located in the Ning'er, Honghe, Baoshan, Lincang, Wenshan, etc. In order to explore the effect of transplanting time on the development and metabolism of Yunyan87 in Ning'er area, we set up 3 treatments, i. e. T1: transplanted 14 days ahead of schedule; T2: transplanted at regular time; T3: transplanted in delay of 14 days. The climate changes for tobacco development caused by different transplanting treatments were recorded; the agronomic traits, internal microstructure, physiological indexes including content of starch,photosynthetic pigments,soluble proteins and soluble sugars,yields and economic incomes of Yunyan87 tobacco under different treatments were measured or observed,and the changes of leaf transcriptome of different treated tobaccos were analyzed by method of RNAseq. The results showed that: different transplanting time resulted in the change of climate and environment, then caused the change of morphology, metabolisms and development of different transplanting time treatments,compared with T1 and T3,T2 had the largest plant height,stem circumference,the numbers of harvesting leaves and leaf areas. The result of microscope observation showed that the leaf blades of T2 are the thickest and the palisade tissue cells number and size, tissue ratio between palisade and spongy tissue are moderate in tobacco proliferating period. Transcriptome analysis result revealed that climate changes causing environment changes of tobacco development led to deferment gene expression among the treated plants and the expression of photosynthesis related genes were up-regulated in T2 compared with T1 and T3,while respiratory and stress tolerance related gene also increased in proliferating period,however the genes related to photosynthesis,respiration,stress tolerance were all down-regulated in T2 in maturation period of the plant. The changes of genes n' expression in both proliferating and maturating of T2 tobacco helped to improve the yield and quality of harvesting leaves which are consistent with the results of T2 has good yield and economic income. The results of current study show that the local cultivation mode for transplanting time is best for Yunyan87 production in Ning'er.