Sanjiang plain wetland is the largest freshwater ecosystem in northeast China, and with its richness in animal and plant species, it displays a high biodiversity. This study provides information about benthic macroinvertebrate diversity and functional groups in association with physicochemical parameters in wetland habitats of Sanjiang plain. Benthic macroinvertebrate samples were collected using a D-frame aquatic net. Shannon-Wiener, Simpson and Pileou's evenness indices were calculated in terms of abundance. The relationship between measured physicochemical variables and benthic macroinvertebrate functional feeding groups (FFGs) was explored using CCA. A total of 57 macroinvertebrate taxa were collected from the 16 sampling sites. Aquatic insects were the most abundant with 11 families, Dytiscidae, Chironomidae, Leptophlebiidae, Belostomatidae, Corixidae, Gerridae, Corduliidae, Gomphidae, Macromiinae, Libellulidae and Phryganeidae. Chironomids were the most diverse and abundant with 26 taxa. The metrics of abundance, Shannon-Wiener, Simpson and Pileou's evenness indices differed significantly among the 16 sampling sites (p = 0.0163, p = 0.0092, p = 0.0474, p = 0.0222, respectively). The findings showed that these 57 benthic macroinvertebrate taxa were categorized in six functional feeding groups, including 19 predators, 15 gathering-collectors, 7 scrapers, 6 filtering-collectors, 5 omnivores and 5 shredders. CCA results displayed that benthic macroinvertebrate functional feeding groups had strong relationships with the physicochemical characteristics in the wetlands of Sanjiang plain.