The accurate estimation of aerodynamic loads is crucial for developing high-speed maglev trains, which can reach speeds of up to 600 km/h. Traditionally, this estimation has been achieved through computational aerodynamic simulation or direct pressure measurement. In this paper, we propose a novel framework for reconstructing transient aerodynamic loads on maglev vehicles using on-board acceleration measurements. In the framework, an inverse mathematical model that correlates the measured acceleration and external aerodynamic loads is derived from a well-calibrated maglev vehicle model. To avoid the ill-posed problem when solving the inverse mathematical model, a multi-task Gaussian Processes method is proposed, in which all reconstructed transient aerodynamic loads are treated as Gaussian Processes and the closed-form posterior distributions of these aerodynamic loads could be calculated. To validate the proposed framework, a set of transient vibration data collected from an operational maglev train passing through a double-track tunnel is utilized for load reconstruction. The results demonstrate that the framework offers a cost-effective and efficient means to obtain aerodynamic loads, highlighting its practical relevance for aerodynamic field testing in the context of evolving high-speed maglev technologies.