Climate change has profound ecological effects, yet our understanding of how trophic interactions among species are affected by climate change is still patchy. The sympatric Atlantic haddock and cod are co-occurring across the North Atlantic. They compete for food at younger stages and thereafter the former is preyed by the latter. Climate change might affect the interaction and coexistence of these two species. Particularly, the increase in sea temperature (ST) has been shown to affect distribution, population growth and trophic interactions in marine systems. We used 33-year long time series of haddock and cod abundances estimates from two data sources (acoustic and trawl survey) to analyse the dynamic effect of climate on the coexistence of these two sympatric species in the Arcto-Boreal Barents Sea. Using a Bayesian state-space threshold model, we demonstrated that long-term climate variation, as expressed by changes of ST, affected species demography through different influences on density-independent processes. The interaction between cod and haddock has shifted in the last two decades due to an increase in ST, altering the equilibrium abundances and the dynamics of the system. During warm years (ST over ca. 4°C), the increase in the cod abundance negatively affected haddock abundance while it did not during cold years. This change in interactions therefore changed the equilibrium population size with a higher population size during warm years. Our analyses show that long-term climate change in the Arcto-Boreal system can generate differences in the equilibrium conditions of species assemblages.