Large-scale Ulva prolifera green tides have successively occurred for 16 years (2007–2022) in the Yellow Sea (YS), and the different life stages of U. prolifera play critical roles in regulating the occurrence and development of green tides. U. prolifera and microalgae have a similar niche in seawater, but their potential interactions are not yet clearly understood. In this study, we investigated the competition relationship between two microalgae and U. prolifera at five different development stages in controlled laboratory experiments. The results showed that one microalgae Alexandrium tamarense, can only inhibit U. prolifera gametes at the first settlement stage. Inversely, the germinated U. prolifera begin to show negative effects on microalgae in multiple ways at the subsequent four stages, and the growth inhibition rates among these stages ranged from 19 to 100%. The complex interactions may influence the formation of green tides. Meanwhile, the potential ecological consequences on phytoplankton, even the decreased occurrence of microalgal blooms in the YS need to be further evaluated.