Because of the limited of experimental condition, there are missing values in gene expression data which make against to following use. Estimating missing values without destroying other data and information lost has becoming an important work of bio-information . By weighted kernel function，similar coefficient between those rows and columns the miss values in and other rows and columns is presented. In this paper an estimation method based on double weighted regression using weighted kernel function is introduced. It makes the information data more abundant by considering gene space correlation and time correlation in regression. Comparing with other methods, weighted double regression method can get better performance.