High entropy alloys (HEAs) have been increasingly attractive as promising next-generation materials due to their various excellent properties. It's necessary to essentially characterize the degree of chemical ordering and identify order-disorder transitions through efficient simulation and modeling of thermodynamics. In this study, a robust data-driven framework based on Bayesian approaches is proposed and demonstrated on the accurate and efficient prediction of configurational energy of high entropy alloys. The proposed effective pair interaction (EPI) model with ensemble sampling is used to map the configuration and its corresponding energy. Given limited data calculated by first-principles calculations, Bayesian regularized regression not only offers an accurate and stable prediction but also effectively quantifies the uncertainties associated with EPI parameters. Compared with the arbitrary determination of model complexity, we further conduct a physical feature selection to identify the truncation of coordination shells in EPI model using Bayesian information criterion. The results achieve efficient and robust performance in predicting the configurational energy, particularly given small data. The developed methodology is applied to study a series of refractory HEAs, i.e. NbMoTaW, NbMoTaWV and NbMoTaWTi where it is demonstrated how dataset size affects the confidence we can place in statistical estimates of configurational energy when data are sparse.