ABSTRACT: Species invasion represents a significant global challenge in terms of both ecological and economic impact. The incursion of Spartina alterniflora and the expansion of Crassostrea gigas in coastal areas has resulted in significant alterations to the habitat, which affected the structure of animal communities. Nevertheless, there remains a paucity of empirical studies examining the mechanisms and impacts of both on food webs. This study focuses on the intertidal zone of Bohai Bay and assesses the impact of the S. alterniflora invasion and the C. gigas reef on food webs. We constructed quantitative food webs from field data, categorizing habitats into pre-S. alterniflora invasion (uninvaded mudflat), post-S. alterniflora invasion (S. alterniflora-dominated), and post-C. gigas appearance (S. alterniflora-C. gigas co-dominated) periods. We found that the presence of S. alterniflora and C. gigas complicated the food web structure by increasing its links and link density. Analyzed from an energy cycling perspective, S. alterniflora reduced mudflat food web energy cycling, while oysters increased post-S. alterniflora invasion energy flow. Additionally, S. alterniflora invasion decreased mudflat food web local stability, and it further reduced by C. gigas aggregations. It is noteworthy that S. alterniflora was incorporated into the food web as a primary producer, primarily mediating trophic interactions. In contrast, C. gigas mainly influenced the food web through non-trophic interactions from habitat modification. The present study offers an empirical case study of the impact of habitat-modifying species on food webs.