The main contribution of this thesis is to propose a Framework to generate Rhythmically- Controlled Multi-Mode Audio-Based Interactive Systems used create variable-form im- provised pieces in real musical performance contexts. In the recent years the field of Interactive Music System has grown considerably but issues related to Rhythm has been underestimated in my point of view. I analyze other related approach and compare them to mine. After that, I develop a profound analysis with respect to Rhythm considering different perspectives. In the core of my work, I develop the concepts of mode and meta- mode of interaction and formalize them using the Theory of Synchronized Automata empowered by Tree Structures. Based on this formalization, I develop computational tools to deal with real life situations. Finally, I describe and analyze two case studies based on their computational structure and practical musical results.