This article proposes a wideband microstrip-to-microstrip vertical transition with multi-layer pixel structures, alongside a multi-branch knowledge-assisted proximal policy optimization (MB-KPPO) method for its automatic design. The proposed transition consists of the three-layer pixel structures with high design degrees of freedom to realize a wide bandwidth. The MB-KPPO adopts a multi-branch policy network instead of a single-branch policy network in the PPO to improve design efficiency. In addition, the MB-KPPO integrates a fully connected shape generation mechanism to incorporate physical requirements. An MS-to-MS vertical multi-layer pixel transition is designed and fabricated by PCB technology. Measurement results show that the multi-layer transition has a frequency range from 3.5 to 17.8 GHz, with a bandwidth that is 25% higher than the single-layer pixel transition towards higher frequencies.