The Yellow River is the longest heavily sediment-laden river in the world, with significant spatial variation in water-sand heterogeneity and corresponding ecological health. In this paper, based on the systematic survey data on benthic macroinvertebrates from 44 sections of the mainstem of the Yellow River in the spring and autumn of 2019, we constructed a system for evaluating the biological integrity of the Yellow River's benthic macroinvertebrates. This system incorporated the ASPT index indicative of the changes in water-sand processes and the relative abundance of individuals in the EPT taxonomic unit, and the scores of the reference point and the impaired point differed significantly, which was suitable for the evaluation of ecological health of a heavily sediment-laden river. The results of the evaluation showed that the proportion of sections in the Yellow River mainstem in a sub-healthy state or above was higher in autumn (75.0%) than that in spring (54.5%). The benthic macroinvertebrate index of biological integrity tended to decrease from the source area downstream. The benthic biotic integrity values of sections in the reservoir area were lower than those of the adjacent natural river sections. Regression analysis showed that the benthic index values of biological integrity of the Yellow River mainstem were negatively correlated with salinity, total nitrogen, urban and agricultural land use, and positively correlated with forest land and grassland use. This study can provide a scientific basis for the evaluation, protection and management of the ecological health of the Yellow River.