The spatial autocorrelation of crop yield violates the independence assumption of conventional methods such as ordinary least square (OLS). Therefore, in the model of crop yield, spatial structure must be incorporated. More often, crop yields are available across space as well as over time, and the additional dimension allows the estimation of the full spatial covariance matrix, using the time dimension. However, the stationarity of the spatial pattern does not necessarily hold over time. In this study, we present empirical evidence that the spatial autocorrelation pattern of cotton yield can be fundamentally changed by the adoption of Bt cotton seeds. The finding of this study provides a cautionary note that spatial autocorrelation may vary over time due to technological change.