The coordination of multiple companies becomes a formidable challenge with the extension of supply chain. For a three-level supply chain comprised of a contract manufacturer (CM), an original equipment manufacturer (OEM), and a retailer, we study the impacts of uncertain yield and uncertain demand on the decisions of pricing, ordering, and production. The Stackelberg game is modeled to derive the optimal decisions. A revenue sharing with shortage penalty contract is subsequently proposed to achieve the coordination of three-level supply chain. We find that there exists a threshold outsourcing price beyond which the CM is motivated to overproduce, otherwise it tends to adopt conservative strategy of producing in accordance with the order. The increase of selling price in any upstream section benefits the seller at the cost of other agents' profits. In contrast, raising price in the end of supply chain brings Pareto improvement to all agents. The coordination mechanism designed in this study enables the flexible profit distribution among all agents in supply chain. In particular, the shortage penalty should be set as the difference between selling price and outsourcing price. The revenue sharing from downstream to upstream can be viewed as the payment transfer which encourages the price reduction from upstream to downstream.