Abstract: Agricultural production has been widely and seriously affected by climate change. In this paper, the logical layers of climate change impacts and adaptation were synthesized based on the interactions of climate system and agricultural ecosystem as well as the social-economic system. The logical layers of climate change impacts could be clarified as the effects due to the change of climate average trend, the enhanced extreme climatic events, ecological consequences and social-economic consequences, then the logical layers of adaptation could be clarified as the high-efficiency use of agro-climatic resources due to warming, systematically adjusting the strategy and technical approaches for disaster reduction and prevention according to the new features of enhanced agro-meteorological disasters, increasing the agricultural climate resilience with the well employment of ecosystem services through the protection of agro-biodiversity and optimizing the agricultural ecosystem’s structure and functions, and transformational update of the agricultural social-economic system. The challenges of agricultural adaptation to climate change were synthesized based on the systematic review of the research progress on the already occurred climate change impacts and the adopted adaptation measures that the climatic stress onto the agricultural system is incessantly enhanced, the vulnerability to climate change is continuously increased, the guarantee system for food security is not complete yet, and the adaptive capacity is still very weak. Finally, the key scientific questions for agricultural adaptation were proposed to enlarge the aspects of climate change impacts assessment, to scientifically identify the vulnerability to climate change and the future climate risk, to reveal the theoretical mechanism of adaptation, to construct the agricultural adaptation system, to strengthen the research on how to increase the capacity of agricultural adaptation decision as well as the implementation of agricultural adaptation actions.