Determining a process-structure-property relationship is the holy grail of materials science, where both computational prediction in the forward direction and materials design in the inverse direction are essential. Problems in materials design are often considered in the context of process-property linkage by bypassing the materials structure, or in the context of structure-property linkage as in microstructure-sensitive design problems. However, there is a lack of research effort in studying materials design problems in the context of process-structure linkage, which has a great implication in reverse engineering. In this work, given a target microstructure, we propose an active learning high-throughput microstructure calibration framework to derive a set of processing parameters, which can produce an optimal microstructure that is statistically equivalent to the target microstructure. The proposed framework is formulated as a noisy multi-objective optimization problem, where each objective function measures a deterministic or statistical difference of the same microstructure descriptor between a candidate microstructure and a target microstructure. Furthermore, to significantly reduce the physical waiting wall-time, we enable the high-throughput feature of the microstructure calibration framework by adopting an asynchronously parallel Bayesian optimization by exploiting high-performance computing resources. Case studies in additive manufacturing and grain growth are used to demonstrate the applicability of the proposed framework, where kinetic Monte Carlo (kMC) simulation is used as a forward predictive model, such that for a given target microstructure, the target processing parameters that produced this microstructure are successfully recovered.