Utilizing the decision model in which neither the power battery producer (PB-producer) nor the new energy vehicle manufacturer (NEV-manufacturer) holds shares as a benchmark, we construct three differential game models with forward shareholding of PB-producer, backward shareholding of NEV-manufacturer, and cross-shareholding of both parties to explore the impact of different shareholding strategies between upstream and downstream firms in a power battery supply chain on the long-term emission reduction decision, the low-carbon advertising input decision, power battery emission reduction level trajectory, low carbon goodwill trajectory, and firm’s profits. The results indicate that: i) if the PB-producer or NEV-manufacturer hold shares in one direction, it only changes its decision variables, but not affects the decision variables of supply chain partners, while if the cross-shareholding is made, the decision level of the firm is higher than that in the one-way shareholding and firms without shareholdings; ii) any shareholding strategies increase the low-carbon goodwill, and if the cross-shareholding is made, the goodwill is the highest; iii) one-way shareholding promotes the profit of the shareholder, and if the marginal profit of the stakeholder is small, the overall profit of the stakeholder will be lower; iv) there exist certain conditions that make the firm’s profit under the cross-shareholding strategy is higher than that under the unidirectional shareholding strategy; v) the variation of emission reduction level, low carbon goodwill and firm’s profits converge to the steady state level over time, and the steady state values are independent of their initial values, which are related to the shareholding strategy in the power battery supply chain. This paper providers management implications for choosing shareholding strategies to improve emission reduction level, low carbon goodwill, and firm’s profits in the power battery supply chain.