Abstract: Investigation of the relationship between crops and the environment as well as their interaction mechanisms at molecular level are the current focus of modern crop cultivation science and molecular ecology. This paper emphasizes ecological properties of genetic molecular and the effect of molecular ecological environment on crop growth and development from the perspective of genetic ecological characteristics of relative gene involvement in the process. It is suggested that scientific technology, policy regulation and control must be implemented based on genetic ecological characteristics at different growth stages of crops to realize high yield, best quality, high efficiency, environment-friendly and security of crop production. Finally, we further discuss several theoretical issues and their research implications on crop molecular ecology.