Cost-effective and high-precision surrogate modeling is a cornerstone of automated industrial and engineering systems. Active learning coupled with Gaussian process (GP) surrogate modeling is an indispensable tool for demanding and complex systems, while the existence of heterogeneity in underlying systems may adversely affect the modeling process. In order to improve the learning efficiency under the regime, we propose the partitioned active learning strategy established upon partitioned GP (PGP) modeling. Our strategy seeks the most informative design point for PGP modeling systematically in twosteps. The global searching scheme accelerates the exploration aspect of active learning by investigating the most uncertain design space, and the local searching exploits the active learning criterion induced by the local GP model. We also provide numerical remedies to alleviate the computational cost of active learning, thereby allowing the proposed method to incorporate a large amount of candidates. The proposed method is applied to numerical simulation and real world cases endowed with heterogeneities in which surrogate models are constructed to embed in (i) the cost-efficient automatic fuselage shape control system; and (ii) the optimal design system of tribocorrosion-resistant alloys. The results show that our approach outperforms benchmark methods.