Indirect species interactions play a critical role in shaping community structure and the functioning of ecosystems. Previous empirical and theoretical studies commonly assumed that indirect interactions were caused in general by changes in population density of interacting species, which is referred to as ‘density-mediated indirect interactions.’ However, there is growing evidence that changes in traits of the individual intermediate species can also be an important mechanism that regulates indirect interactions among species, and ecologists term these species interactions ‘trait-mediated indirect interactions’ (TMⅡs). TMⅡs are prevalent in both aquatic and terrestrial systems, and their effects are often as strong as, or stronger than, those of density-mediated indirect effects. Studies on the characteristics, causes, and consequences of TMⅡs are essential to understand the complexity and diversity of multispecies interactions in natural ecosystems fully. In this paper, we summarize the concept and classification of TMⅡs, and suggest that trait plasticity and species specificity are the two intrinsic mechanisms for the occurrence of TMⅡs. We also review the direct evidence for TMⅡs in various permutations of interaction webs that can have both trophic and non-trophic links, and then highlight the profound effects of TMⅡs on regulation of ecological functions and processes in a wide range of ecological systems. Finally, we propose future developments regarding the effects of TMⅡs to provide a reference framework for related research.