Recently, much research has focused on lowering carbon emissions in logistics. This paper attempts to contribute to the literature on the joint shipment size and carbon reduction decisions by developing novel models for distribution systems under direct shipment and peddling distribution strategies. Unlike the literature that has simply investigated the effects of carbon costs on operational decisions, we address how to reduce carbon emissions and logistics costs by adjusting shipment size and making an optimal decision on carbon reduction investment. An optimal decision is made by analyzing the distribution cost including not only logistics and carbon trading costs but also the cost for adjusting carbon emission factors. No research has explicitly considered the two sources of carbon emissions, but we develop a model covering the difference in managing carbon emissions from transportation and storage. Structural analysis guides how to determine an optimal shipment size and emission factors in a closed form. Moreover, we analytically prove the possibility of reducing the distribution cost and carbon emissions at the same time. Numerical analysis follows validation of the results and demonstrates some interesting findings on carbon and distribution cost reduction.