Understanding how energy and matter flow among habitats is a central issue in ecology. In lake ecosystems, benthic-pelagic coupling (B-P coupling) was mainly studied based on the diets of top consumers at a population level or through food chains. However, how B-P coupling operates at the ecosystem level is largely unknown. In the present study, we revealed B-P coupling within an energetic food web framework, combining stable isotope analyses and mass balanced model. We constructed the energetic food webs of two large shallow lakes of different trophic status based on field survey data. We also defined benthic and pelagic components based on the proportion of consumer energy uptake from phytoplankton (benthic: < 50%; pelagic: > 50%; benthivore: < 20%; planktivore: > 80%; coupler: 20-80%) and quantified the energy flux through B-P coupling in the two lake food webs. The total consumption was estimated to be 699 t/km(2)/y in Lake Erhai (mesoeutrophic lake) and 2094 t/km(2)/y in Lake Dianchi (hypereutrophic lake), and the B-P coupling energy was 405 t/km(2)/y and 213 t/km(2)/y, re-spectively. In these lakes, B-P coupling occurred on multiple trophic levels; lower trophic level consumers contributed the largest proportion (90% and 98%), while top consumers were of limited importance; most coupling links were weak, and energy exchange was highly asymmetric with the total amount of energy exported from benthic part to pelagic part being over 4 folds of the counter flux. The quantity and pattern of B-P coupling vary between the mesoeutrophic and hypereutrophic lakes. In terms of energy flux per unit area, the total system throughput in the mesoeutrophic lake (Lake Erhai) was 3.73 times of that in the hypereutrophic lake (Lake Dianchi), while the proportion of coupling energy was much lower in the former (19%) than the latter (31%). A greater energy flux through pelagic-to-benthic pathways was found in the hypereutrophic lake, and most of the coupling energy was contributed by consumers at higher trophic levels. Besides, the coupling strength was stronger in the hypereutrophic than the mesoeutrophic lake. We showed for the first time how B-P coupling operates in lake energetic food webs. Our results provided new insights into understanding the energy flux through B-P coupling of lake ecosystems, and how such coupling could be changed by environmental disturbances. We also provided a new approach to reveal habitat coupling within an energetic food web framework.