Climate change has been proven to be the ultimate cause of social crisis in pre-industrial Europe at a large scale. However, detailed analyses on climate change and macro-economic cycles in the pre-industrial era remain lacking, especially within different temporal scales. Therefore, fine-grained, paleo-climate, and economic data were employed with statistical methods to quantitatively assess the relations between climate change and agrarian economy in Europe during AD 1500 to 1800. In the study, the Butterworth filter was adopted to filter the data series into a long-term trend (low-frequency) and short-term fluctuations (high-frequency). Granger Causality Analysis was conducted to scrutinize the associations between climate change and macro-economic cycle at different frequency bands. Based on quantitative results, climate change can only show significant effects on the macro-economic cycle within the long-term. In terms of the short-term effects, society can relieve the influences from climate variations by social adaptation methods and self-adjustment mechanism. On a large spatial scale, temperature holds higher importance for the European agrarian economy than precipitation. By examining the supply-demand mechanism in the grain market, population during the study period acted as the producer in the long term, whereas as the consumer in the short term. These findings merely reflect the general interactions between climate change and macro-economic cycles at the large spatial region with a long-term study period. The findings neither illustrate individual incidents that can temporarily distort the agrarian economy nor explain some specific cases. In the study, the scale thinking in the analysis is raised as an essential methodological issue for the first time to interpret the associations between climatic impact and macro-economy in the past agrarian society within different temporal scales.