In this paper, the evaporation of sessile droplets resting on a substrate with different thermal properties is numerically investigated. Computations are based on a transient axisymmetric numerical model. Special attention is paid to evaluate thermal effects of substrate on the structure of bulk fluid flow in the course of evaporation. Numerical results reveal that Marangoni convection induced by non-uniform distribution of temperature along the interface exhibits three distinctly different behaviours: inward flow, multicellular flow and outward flow, consequently resulting in different particle depositions. It is highlighted that three factors (i.e. relative thermal conductivity, relative substrate thickness and relative substrate temperature) strongly affect the flow pattern. In order to further investigate the coupling effects of different influential factors, a Kriging-based response surface method is introduced. We model the flow behaviour as a function of continuous influential factors using a limited number of computations corresponding to discrete values of the inputs. The sensitivities of the Marangoni flow are also analysed using Sobol’ index to study the coupling mechanisms of influential factors. The proposed method can be used to forecast the flow patterns for any input parameter without additional sophisticated computer simulation, and allows to confidently estimate an unknown environmental parameter.