A green scheduling problem is proposed in this work, where both constraints on intermediate storage capacity and job transportation requirements are simultaneously considered. An improved discrete pathfinder algorithm (IDPFA) with multi-neighborhood local search is proposed to minimize the maximum completion time and total energy consumption. The algorithm addresses the green flow shop scheduling problem with limited buffers and automated guided vehicle (GFSSP_LBAGV). Firstly, based on the machine speed constraints, the transportation time for moving jobs by the automated guided vehicle (AGV) is incorporated to establish a mathematical model. Secondly, the core idea of the pathfinder algorithm (PFA) is applied to the evolutionary process of the discrete PFA, where three different crossover operations are used to replace the exploration process of the pathfinder, the influence of the pathfinder on the followers, and the mutual learning among the followers. Then, a multi-neighborhood local search is employed to conduct a detailed exploration of high-quality solution spaces. Finally, extensive standard test sets are used to verify the effectiveness of the proposed IDPFA in solving GFSSP_LBAGV.