Breakthrough innovation is an important means of promoting leapfrog development in technology and encouraging the transformation and advancement of industry. Understanding the formation mechanism underlying this phenomenon provides a theoretical reference for overcoming the "bottleneck" problem with respect to key core technologies. Based on catastrophe theory, this paper constructs a formation mechanism model of breakthrough innovation and argues that the formation path of the "accumulation stage-progressive stage-critical stage-mutation stage" of breakthrough innovation mainly depends on the degree to which internal and external knowledge resources are aggregated. From the perspective of knowledge collaboration, this paper constructs a system dynamics model to systematically investigate the dynamic process leading from knowledge resources to innovation breakthrough. It is found that the smooth introduction of external knowledge resources is the primary driving factor that allow enterprises to realize breakthrough innovation, which is of great significance for enterprises to solve the problems of path dependence and resource constraints of breakthrough innovation. Absorptive capacity and aggregation capacity are key capabilities that can allow enterprises to facilitate breakthrough innovation. However, excessive organizational memory and knowledge inertia can crystallize organizations’ mode of operation and inhibit the formation of breakthrough innovation. The research conclusion provides an operable methodology for the successful implementation of breakthrough innovation in enterprises, and contributes to the successful transition of technological behavior from the original technological track to the new technological track.