The interactive relationships between cities in the knowledge economy era have attracted much attention. Researchers have applied a range of methods to explore intercity innovative relationships and associated network characteristics. It nevertheless remains unclear just how intercity innovative relationships can be theoretically constructed based on knowledge flow space and how further scientific simulation methods can be designed. Research questions in this area have rarely been explored in detail, an issue which has inevitably placed obstacles on further exploration. A framework for the theoretical construction of intercity innovative relationships is presented in this study; the basis for this research is that an intercity innovation network is essentially a 'soft network', distinct from a 'hard network'. These interconnections are founded on a subjective relationship construction process and therefore necessitate scale transformation from 'point-point' connections between innovative subjects in different cities with respect to 'city-city' interactions. At the same time, this transformation process is prone to exaggerations and deviations from objective intercity innovative relationships and therefore exerts considerable influence on the accuracy of results such that constructions must be entirely theoretical. Four construction methods for intercity innovative relationships and network simulation are summarized in this study, including an intercity undirected network based on cross-city co-operations between scientific and technological achievements, an intercity directed network based on the cross-city transfer of scientific and technological achievements, an intercity innovation network based on the cross-city flow of high-end talents, and an intercity innovation network based on the multi-city distribution of innovative enterprises and institutions. Simulation tests were then undertaken using relevant data to reflect aspects of these relationships. The results of this analysis are conducive to further exploration of global and regional innovative spatial patterns from the perspective of urban geography and intercity relationships and provide a theoretical and methodological foundation for further research on intercity innovation networks.