The classical joint economic lot-sizing (JELS) policy in a single-vendor single-buyer system generates an equal production quantity in all cycles, where the input parameters remain static indefinitely. In this paper, a new two-echelon supply chain inventory model is developed involving a hybrid production system. The proposed model simultaneously focuses on green and regular production methods with an optimal allocation fraction of green and regular productions. Unlike the classical mathematical formulation, cycles do not depend on each other, and consequently, each model parameter can be adjusted to be responsive to the dynamic nature of demand rate and/or price fluctuation. A rigorous heuristic approach is used to derive a global optimal solution for a joint hybrid production system. This paper accounts for carbon emissions from production and storage activities related to green and regular produced items along with transportation activity under a multi-level emission-taxing scheme. The results emphasize the significant impact of green production on emissions. That is, the higher the allocation fraction of green production, the lower the total amount of emissions generated by the system, i.e., the system becomes more sustainable. Adopting a hybrid production method not only decreases the greenhouse gas (GHG) emissions dramatically, but also reduces the minimum total cost per unit time when compared with regular production. One of the main findings is that the total system cost generated by the base closed-form formula of the proposed model is considerably lower in the first cycle (subsequent cycles) than that of the existing literature, i.e., 33.59% (16.13%) when the regular production method is assumed. Moreover, the optimal production rate generated by the proposed model is the one that minimizes the emissions production function. In addition, the system earns further revenue by utilizing a mixed transportation policy that combines the Truck Load (TL) and Less than Truck Load (LTL) services. Illustrative examples and special cases that reflect different realistic situations are compared to outline managerial insights.