The Arabidopsis thaliana population has been exposed to unexperienced biotic and abiotic stresses as a result of range expansion or environmental change. To obtain a global picture of the genetic adaptations in the population history of A. thaliana, we constructed a database of the phenotypic-adaptations (p-adaptations) and gene expression-adaptations (e-adaptations). We analysed the dynamics of the allele frequencies at the 23,880 QTLs of 174 traits and 8,618 eQTLs of 1,829 genes with respect to the total SNPs in the genomes, and identified 650 p-adaptations and 3,925 e-adaptations (FDR=0.05). The population underwent large scale p-adaptations and e-adaptations along four lineages, the eastward migration to Central Asia and South Siberia, Russia, the northward migration to Sweden, the migration to Azerbaijan, and the migration of the German population to the United States. Extremely cold winters and short summers prolonged seed dormancy, and expanded the root system architecture. Low temperatures prolonged the growing season and low light intensity required the increased chloroplast activity. The subtropical and humid environment enhanced phytohormone signaling pathways in response to the biotic and abiotic stresses. Exposure to heavy metals selected for alleles underlying low heavy metal uptake from soil, lower growth rate, lower resistance to bacteria, and higher expression of photosynthetic genes were selected. The database of p-adaptations and e-adaptations, which complements studies focusing on specific aspects of adaptation, may be useful for future studies to understand the biological adaptations of A. thaliana throughout its population history.