In this paper, we consider the shape inverse problem of a body immersed in the incompressible fluid governed by thermodynamic equations. By applying the domain derivative method, we obtain the explicit representation of the derivative of solution with respect to the boundary, which plays an important role in the inverse design framework. Moreover, according to the boundary parametrization technique, we present a regularized Gauss–Newton algorithm for the shape reconstruction problem. Finally, numerical examples indicate the proposed algorithm is feasible and effective for the low Reynolds numbers. Copyright © 2017 John Wiley & Sons, Ltd.