Under the carbon cap-and-trade mechanism, we consider an emission-dependent supply chain consisting of a supplier, a manufacturer, and a 3PL firm that adopts variable transportation fee strategy. Five models on the basis of the supplier and manufacturer with or without capital constraints are considered to discuss members’ optimal decisions. The insights are obtained as follows. First, the ordering quantity under 3PL financing service is larger than that under two firms are well-funded when the transportation fee or carbon emission is less than a certain constant. The variable transportation fee strategy and members’ carbon emission reduction behavior are beneficial to each supply chain participant. Second, the carbon emissions of members decide whose capital constraint is more beneficial to 3PL firm, and 3PL prefers to cooperate with a medium rich manufacturer (rich supplier). Third, the external financing modes are analyzed to get the 3PL financing service can create new value for the manufacturer and 3PL if the transportation fee is below a threshold, and this threshold increases with the manufacturer’s carbon emission. When the transportation fee is larger than a threshold, a capital-constrained supplier will choose bank financing, and this threshold decreases with the supplier’s carbon emission. Finally, we demonstrate that the manufacturer’s loss aversion (carbon cap) can increase (decrease) its bankruptcy threshold.