In this study, an inverse conjugate heat transfer problem is examined to estimate temporally and spatially the dependent unknown surface heat flux using thermography techniques with a thermal camera in a three-dimensional domain. Thermography techniques encompass a broad set of methods and procedures used for capturing and analyzing thermal data, while thermal cameras are specific tools used within those techniques to capture thermal images. In the present study, the interface conditions of the plate and air domains are obtained using perfect thermal contact conditions, and therefore we define the problem studied as an inverse conjugate heat transfer problem. Achieving the simultaneous solution of the continuity, Navier–Stokes, and energy equations within the air domain, alongside the heat conduction equation in the plate domain, presents a more intricate challenge compared to conventional inverse heat conduction problems. The validity of our inverse solutions was verified through numerical simulations, considering various inlet air velocities and plate thicknesses. Notably, it was found that due to the singularity of the gradient of the cost function at the final time point, the estimated results near the final time must be discarded, and exact measurements consistently produce accurate boundary heat fluxes under thin-plate conditions, with air velocity exhibiting no significant impact on the estimates. Additionally, an analysis of measurement errors and their influence on the inverse solutions was conducted. The numerical results conclusively demonstrated that the maximum error when estimating heat flux consistently remained below 3% and higher measurement noise resulted in the accuracy of the heat flux estimation decreasing. This underscores the inherent challenges associated with inverse problems and highlights the importance of obtaining accurate measurement data in the problem domain.