Objective To understand the difficulties faced by reproductive-age women with inflammatory bowel disease (IBD) in fertility decision-making, and to provide reference for clinical practitioners to support decision-making. Methods Through in-depth semi-structured interviews with 14 reproductive-age women with IBD, this phenomenological study was used to examine the perceptions of decision-making about fertility. Data were analyzed via Braun and Clarke′s style of thematic analysis. Results Two themes and seven sub-themes emerged:subjective perceptions of difficulty (decision-making intention, cognitive bias, role conflict, and negative emotions) and objective restrictions (supportive environment, childbirth costs, and behavior consequence). Conclusion Reproductive-age women with IBD have subjective and objective difficulties in decision-making about fertility. Medical staff should help them change misconceptions, alleviate their negative emotions, develop decision aids to support fertility decision-making, and provide systematic support and interventions, to relieve their decision-making difficulties.