Diffusive‐convection (DC) staircases, characterized by interleaving well‐mixed layers and high‐gradient interfaces of thermohaline properties, are commonly observed in the Canada Basin, Arctic. Previous studies suggested a quasi‐steady state of the thermohaline structures of these staircases. In this work, we employ mooring and Ice‐Tethered Profiler (ITP) data to show emergent merger events of staircases mediated by subsurface eddies with warm cores located at 300–500 m depths in 2005, 2007 and 2009. Two types of merger events, the B‐merger (resulting from strengthening of stronger interfaces at the expense of weaker ones) and the H‐merger (produced by vertical drift and collision of staircase interfaces), are documented during the passage of subsurface eddies. The merging staircases are located at 320–450 m depths, with layers of up to 70 m thick and high‐gradient interfaces thinner than 5 m. Mooring measurements reveal the emergence of staircase mergers associated with a background Richardson number dropping from a typical magnitude of – to , indicating the persistence of DC staircases in the presence of strong shears. In parallel, ITP data suggest the formation of B‐mergers (H‐mergers) to be favored within the eddy core (flank). The vertical heat fluxes associated with the B‐merger (H‐merger) staircases are estimated to be ∼3 W/m2 (∼1.5 W/m2), which substantially exceed the typical staircase‐driven heat fluxes of W/m2. These observations imply the significance of subsurface eddies in shaping the halocline structures and thus the vertical heat fluxes in the Arctic Ocean, particularly in a warming climate.