Cultivated land protection (CLP) entered the new era of macro administration in 1999 in China. This paper presents a holistic analysis of cultivated land use change concerning the three goals of the CLP, i.e., grain security, ecological security and harmonizing regional development. Farmers’ willingness to grow grain has been the key factor in safeguarding grain security. Grain-for-green policy has contributed to improving ecological state especially in the western provinces. Effects of the land macro-control of the CLP on harmonizing regional development were significant. Moreover, cultivated land use change in 1999-2007 points out the way of the evolving policy in the future. From the viewpoint of normative concept of multifunctionality, we discuss development of the three land functions, i.e., production function, environmental function and carrier function. Finally, we propose to emphasize multifunctional land management based on regional differences to promote transition of the CLP.