The co-evolution of fig wasps with fig trees provide an excellent model for studying ecological systems and adaptive evolution. Transposable elements (TEs), as an important component of the genomes, are the powerful driver for environmental adaptation of the organisms. Here, the TEs in the genomes of six pollinator and five non-pollinator species were analyzed in the characteristics of composition, historical burst patterns, and their possible effects on the functions of conjunctive genes. Compared with pollinators, non-pollinators’ TEs showed a significant burst state with more types, longer lengths, and higher contents in the genomes, which might be related to their different evolutionary and life histories, as well as their different sensitivity to environmental changes. However, we identified a common TE burst peak period of 32-34 Mya in both groups, highly consistent with the glacial epoch of Eocene-Oligocene transition in geological history. Further functional enrichment analysis of the genes within 1 Kb near the insertion positions of TEs in the four geological periods representing the major continental ice sheet growth or decay was demonstrated, and the results showed that large amount of TEs were inserted near genes related to the environmental information processing, especially the Circadian entrainment pathway. These TEs might act as cis-regulatory modules to regulate the conjunctive genes in response to geo-climate changes. These results revealed the molecular basis of the fig wasp’s response to changes in the syconia microenvironment and paleoclimate macroenvironment from the perspective of genomic TEs. Keywords: transposable elements, fig wasp, adaptive evolution, geo-climate, cis-regulatory modules