In the process of evolution in Start-up Enterprises, its social networks will often occurred Mutations phenomenon because of environmental changes, the changing conditions, the reverse direction, management of error, etc. This paper analyzed the evolution in social network of Start-up Enterprises through the basic concepts of the theory of mutations, definition of mutations in Start-up Enterprises′ social network evolution, and the using of swallow-tail mutation theory; proposed countermeasures of how to make full use of social network to facilitate Start-up Enterprises timely and accurately identify mutations, take measures, reduce the loss which mutations brought.