The article presents a numerical model for moving boundary conjugate heat transfer in stratified twofluid flows with a growing deposit layer. The model is applicable to other general moving boundary conjugate heat transfer problem in a two-fluid flow environment with deposition occurring simultaneously. The level-set method is adopted to capture the fluid-fluid interface and fluid-deposit front. The governing equations are solved using a finite volume method. Upon verification of the model, the effects of inlet velocity ratio, Damköhler number and thermal conductivity ratio on the flow, deposition as well as heat transfer are investigated. Generally, Nusselt number on the lower wall, Nulx and upper wall, Nuux show distinct features with the change of these parameters. Nuux increases with the increase of fluid 1 inlet velocity and the thermal conductivity of deposit layer, respectively. While it decreases with the increase of Damkholer number. Unlike the variation trend of Nuux, Nulx varies differently in the upstream and downstream along the channel, respectively under these parameters. A high fluid 1 velocity and a high thermal conductivity of deposit layer have a high Nulx upstream and a low Nulx downstream. However, a high Damkholer number results in a low Nulx upstream and a high Nulx downstream.