In the low carbon economy, the cost structure and profit model of traditional manufacturing industry have been completely overturned. The production decision and coordination of the closed-loop supply chain with remanufacturing and carbon emission reduction deserve attention. Under three different channel power structures, closed-loop supply chain decision models with retailer holding manufacturer's emission reduction investment are constructed. Then the effects of power structures and equity cooperation on the production decision and enterprise profit are analyzed. Finally, the coordination effect of equity cooperation and two-part tariff are discussed. It is shown that the closed-loop supply chain with different power structure needs to choose the appropriate shareholding ratio. Under the dominant retailer power structure, the higher shareholding ratio produces higher recovery rate, carbon emission reduction and market demand, while in the Nash game, it is just the opposite. In the power structures with a leader, the increase of retailer's shareholding ratio can improve the profit of the leading enterprise, while in the power structure without a leader, the increase or decrease of enterprise profits is affected by both shareholding ratio and consumers' low-carbon preference. No matter what power structures, equity cooperation can only partially coordinate the closed-loop supply chain, and perfect coordination can be achieved through two-part tariff contracts.