The Authors has Commented the Complexity of Supply Chain Networks in Manufacturing Industry Based on Complex Network Theory.Complex Supply Chain Networks in Manufacturing Industry has Characteristics of Small-World and Scale-Free. the Authors has Discussed Various Uncertainties of Complex Supply Chain Networks in Manufacturing Industry. and has Analyzed Spread and Control of Uncertainty of Complex Supply Chain Network in Manufacturing Industry. the Research Showed that Shorten Delivery Lead Times and Strengthen the Exchange of Information can Effectively to Improve Enterprises Cope with Uncertainty Ability, which has Important Role to Control Uncertainty Occurrence in Manufacturing Manufacturing Complex Supply Chain Networks in Manufacturing Industry.