A long-term assessment of the benthic habitat quality of intertidal flats in Liaohe Estuary was conducted by three integrating ecological indices, AZTI’s Marine Biotic Index (AMBI), Multivariate-AMBI (M-AMBI), and Shannon–Wiener diversity index (H′) based on macrobenthos data from 2013 to 2020. The results showed that the macrobenthic communities were characterized by indifferent and sensitive species of AMBI ecological groups. The annual ranges of H′, AMBI, and M-AMBI were 0.77–1.56, 1.44–3.73 and 0.36–0.54, respectively. Noticeable differences were found among assessment obtained by these biotic indices. Approximately 100%, 24%, and 78% sampling sites had “moderate”, “poor”, and “bad” statuses as assessed by H′, AMBI, and M-AMBI, respectively. Compared with H′ and AMBI, M-AMBI may be more applicable to evaluate the benthic habitat quality of intertidal flats in Liaohe Estuary. Results suggest that the benthic habitat quality in the middle parts of intertidal flats still had an unacceptable status and has not improved radically to date after large-scale “mariculture ponds restored to intertidal flats”.