The likelihood of failure in disruptive technological innovation remains remarkably high, and the underlying causes of such innovation dilemmas have not yet been systematically addressed. Adopting paradox as a meta-theoretical lens, this paper investigates, from the perspective of the innovation chain, the conditions under which latent paradoxical tensions become salient, their typologies, governance strategies, and intrinsic logic therein. Specifically, the inherent plurality, change, and scarcity of disruptive technological innovation activities constitute the conditions rendering paradoxes salient. Subsequently, this paper proposes two sets of paradoxes—strategic paradoxes and operational paradoxes—along with their specific constituent types, and posits that innovation failure represents the adverse consequence of salient paradoxes. Furthermore, through governance strategies, contradictory elements can be effectively integrated and coordinated, thereby enabling the resolution of innovation dilemmas. The findings provide new theoretical insights and practical implications for advancing disruptive technological breakthroughs and cultivating new quality productive forces in China.