Collaboration represents an increasing tendency among Small and Medium Enterprises (SMEs), since the possibility of being a cooperative partner of a network allows the achievement of development strategies, either to improve production processes or to increase competitiveness. The objective of the paper is to propose and apply a new methodology to model manufacturing SME networks in terms of graph matrices, in order to identify some conditions that can foster an effective collaboration among partners of a SME network. A classification of SME networks in four typologies named “Marshallian Network”, “Supply chain network”, “Hub and Spoke network” and “Scientific Park” will be introduced. For each typology a graph-based model will be used to find out limits and critical points that can hinder the SME collaboration, or focal points for the interaction reinforcing.