With the rapid development of the economy, pollution of the coastal marine environment has become increasingly serious, resulting in an evident decline in environmental quality and deterioration of ecosystems, which have harmful effects on biological resources and human health. Benthic foraminifera, as indicator organisms of marine environments, have the characteristics of small size, wide distribution, high density and species diversity, short life cycles, good preservation potential in marine sediments, and high sensitivity to various pollutants, all of which play an important role in monitoring marine environmental pollution and changes in marine ecosystems. In this study, we reviewed the effects of natural environmental factors, such as temperature, salinity, dissolved oxygen, sediment grain size, organic matter, and water depth and anthropogenic pollutants, such as heavy metals, organic pollutants, and nutrients on the shell morphology, species abundance, community composition, and diversity of benthic foraminifera. We summarized the response indicators of benthic foraminifera to marine environmental changes. The microscopic characteristics of the benthic foraminifera, such as pore density, porosity, and chemical composition, such as Mg/Ca and B/Ca, can be used to indicate marine climate changes, including ocean warming, ocean acidification, and low oxygen. Decrease in benthic foraminiferal community diversity, increase in tolerant species abundance, and decrease in sensitive species abundance can be used as indicators of marine environmental pollution. In addition, we pointed out problems that require attention and directions for future research. Currently, most foraminiferal studies use different techniques and methods. The lack of standardized methods for sample collection, preparation, processing, and data analysis makes it impossible to compare the results of most studies. In addition, the response mechanisms of benthic foraminifera to environmental changes are unclear. Therefore, future studies should explore the genetic mechanisms of benthic foraminiferal responses to environmental changes at the gene level by integrating genomics, transcriptomics, and proteomics with species ecology. The purpose of this study was to provide a theoretical basis for using benthic foraminifera to reconstruct and predict marine climate change and indicate modern marine environment quality.