This study integrates firms’ innovation and advertising decisions in a two-echelon supply chain, where a monopoly manufacturer sells products to ultimate consumers through an autonomous retailer. Considering that both innovation and advertising contribute to the product demand, we first investigate the optimal equilibriums of channel members under two different game structures: the non-cooperative and cooperative. In the non-cooperative structure, the manufacturer controls the innovation effort and wholesale price while the retailer controls the advertising rate and retail pricing. In the cooperative structure, the manufacturer agrees to share part of retailer’s advertising expenditure. We find that both the optimal operation and marketing decisions are sensitive to effects of innovation and advertising on demand as well as the manufacturer’s cost reduction coefficient due to innovation. Further, we find that the manufacturer always prefers cooperation. Meanwhile, only when the firms’ investments significantly contribute to the market mechanism, does the retailer have incentive to implement a cooperative program. In addition, we further propose a new two-way subsidy policy to coordinate channel members’ business functions.