With the aim of reducing cost, carbon emissions, and service periods and improving clients’ satisfaction with the logistics network, this paper investigates the optimization of a variant of the location-routing problem (LRP), namely the regional low-carbon LRP (RLCLRP), considering simultaneous pickup and delivery, hard time windows, and a heterogeneous fleet. In order to solve this problem, we construct a biobjective model for the RLCLRP with minimum total cost consisting of depot, vehicle rental, fuel consumption, carbon emission costs, and vehicle waiting time. This paper further proposes a novel hyper-heuristic (HH) method to tackle the biobjective model. The presented method applies a quantum-based approach as a high-level selection strategy and the great deluge, late acceptance, and environmental selection as the acceptance criteria. We examine the superior efficiency of the proposed approach and model by conducting numerical experiments using different instances. Additionally, several managerial insights are provided for logistics enterprises to plan and design a distribution network by extensively analyzing the effects of various domain parameters such as depot cost and location, client distribution, and fleet composition on key performance indicators including fuel consumption, carbon emissions, logistics costs, and travel distance and time.