The spatial extent and incidence of Lyme disease is increasing in the United States, particularly in the Upper Midwest and Northeast. Many previous studies have explored the drivers of its spatial pattern, however, few studies tried to explore the drivers for the changes of Lyme disease. We here compared the spatial patterns of changes of human Lyme cases and incidence in the Northeast and Upper Midwest between 2003–2005 and 2015–2017, and applied two different approaches (i.e., a statistical regularization approach and model averaging) to investigate the climatic and landscape factors affecting the risk change between the two periods. Our results suggested that changes in land-use variables generally showed different relationships with changes of human Lyme risk between the two regions. Changes of variables related to human-use areas showed opposite correlations in two regions. Besides, forest area and forest edge density generally negatively correlated with the change of human Lyme risk. In the context of ongoing habitat change, we consider this study may provide new insight into understanding the responses of human Lyme disease to these changes, and contribute to a better prediction in the future.