Generative artificial intelligence (GenAI) is reshaping the research paradigm of doctoral education, with growing evidence suggesting that the use of artificial intelligence (AI) tools could promote innovative behaviour among doctoral students. However, the use of AI tools in scientific research should be approached with special caution, as improper use may lead to ethical issues in scientific research, underscoring the importance of artificial intelligence literacy (AI literacy). This study examined the impact of AI literacy on the innovative behaviour of doctoral students, proposing a theoretical model of 'AI literacy-innovative behavior' from the perspective of technology affordance. Specifically, it explored the chain mediating effect of AI affordance and emotional engagement between AI literacy and doctoral students' innovative behaviour. This study investigated 354 doctoral students from three Chinese universities and tested the proposed theoretical model through partial least squares structural equation modelling (PLS-SEM). Results indicate that AI literacy has a significant positive impact on innovative behaviour, AI affordance and emotional engagement both serve as mediators in the relationship between AI literacy and innovative behaviour, and AI affordance and emotional engagement play a chain mediating role in the relationship between AI literacy and innovative behaviour. These findings provide valuable theoretical insights into the mechanisms through which AI literacy influence innovative behaviour and offer practical implications for promoting responsible AI usage in doctoral research contexts.