In the sustainable operation process of innovation alliances, there are two developmental trends: organizational stability and organizational change. These two mutually exclusive characteristics have a paradoxical impact on both the innovation performance and the sustainable development of alliances. To further examine this paradoxical relationship, we create a research model examining the impact of organizational change and organizational stability on alliance innovation performance, we also examine how this relationship is moderated by environmental uncertainty. We validate the theoretical assumptions through a questionnaire survey analysis of 311 Chinese enterprises. The results indicate that both the organizational change and organizational stability of innovation alliances have an inverted U-shaped impact on alliance innovation performance. Environmental uncertainty strengthens the impact of organizational change on alliance innovation performance, causing the inflection point of the curve to shift leftward and its shape to become steeper. On the other hand, environmental uncertainty weakens the impact of organizational stability on alliance innovation performance, causing the inflection point of the curve to shift rightward and its shape to become gentler. We contribute valuable insights for balancing the paradoxical relationship of alliances and strategic innovation choices under environmental uncertainty.