The ship pipe workshop stands out as the complicated production system, which operates with characteristics like multi-factory configuration, multi-mobile resource and multi-processing mode. Stemming from the bottleneck issue of ship pipe production and the urgent demand for green intelligent production, this paper investigates a distributed heterogeneous energy-efficient flexible flowshop scheduling, where the limited mobile resource, permutation flowshop and flexible flowshop are explicitly and simultaneously taken into account. With the integration of multiple goals and complex constraints, an integer programming model is well-established, aiming to minimize the makespan and total energy consumption simultaneously. To address this problem, an effective shuffled frog leaping differential evolution algorithm, named SFL-DEA, is proposed. Within the SFL-DEA, an innovative good-point set initialization is well-designed to improve the initial solution group. To further promote the searchability of SFL-DEA, we introduce several effective operations, including hybrid self-adaptive double differential strategy, bidirectional crossover strategy and modified shuffled frog leaping algorithm. Extensive experiments and comparisons corroborate the effectiveness and versatility of the presented SFL-DEA in addressing the studied problem. The findings are very valuable to curtail the delay cost and promote the environmental pollution issue for manufacturing industries especially in the ship pipe workshop.