Fruit shape and color are two important quality traits of fruits.Auxin was considered as an important factor in fruit formation and expansion.HID-Ⅲ is a hyper gene family in plants which was reported involved in meristem maintenance,auxin transportation and cell identification,part of its family members were regulated by miR166.MiR166 is a conserved microRNA in plants.Fruit specific expressing miR166 which derived by 2A11 in tomato resulted reduced fruit height in transgenic plants compared to wild type.Moreover,the repression effect of lateral shooting in 2A11::miR166 was suppressed during early flowering time which was similar to the phenotype observed in exogenously supplied with NPA(an auxin transportation inhibitor)in wild type.Interestingly,in 2A11-miR166 transgenic plants,significantly reduction of epidermal hair and abnormity of cell differentiation in fruit,and color changed in mature fruit were observed.The reduction of height,the abnormity in fruit epidermal hair and cell differentiation were connected to phytohormone auxin,the expression of auxin transporting factors(PINs)and auxin response factors(ARFs)were investigated in 2A11-miR166 transgenic plants and the ChiP-Seq of SIREV(target of miR166)was implored the potential mechanism of regulation fruit quality in tomato.Our results contributed the understanding of the underlying mechanism of interaction of miRNA and auxin during fruit formation and color change in tomato.