In the Integrated Circuit (IC) design flow, floorplanning (FP) determines the position and shape of each block. Serving as a prototype for downstream tasks, it is critical and establishes the upper bound of the final PPA (Power, Performance, Area). However, with the emergence of 3D IC with stacked layers, existing methods are not flexible enough to handle the versatile constraints. Besides, they typically face difficulties in aligning the cross-die modules in 3D ICs due to their heuristic representations, which could potentially result in severe data transfer failures. To address these issues, we propose FlexPlanner, a flexible learning-based method in hybrid action space with multi-modality representation to simultaneously handle position, aspect ratio, and alignment of blocks. To our best knowledge, FlexPlanner is the first learning-based approach to discard heuristic-based search in the 3D FP task. Thus, the solution space is not limited by the heuristic floorplanning representation, allowing for significant improvements in both wirelength and alignment scores. Specifically, FlexPlanner models 3D FP based on multi-modalities, including vision, graph, and sequence. To address the non-trivial heuristic-dependent issue, we design a sophisticated policy network with hybrid action space and asynchronous layer decision mechanism that allow for determining the versatile properties of each block. Experiments on public benchmarks MCNC and GSRC show the effectiveness. We significantly improve the alignment score from 0.474 to 0.940 and achieve an average reduction of 16% in wirelength. Moreover, our method also demonstrates zero-shot transferability on unseen circuits.