Currently, the problem of heavy metal pollution in China is becoming increasingly serious, which poses grave threats to the environment and human health. Owing to the non-biodegradability and toxicity of heavy metals, a more sustainable and ecological approach to remediate heavy metal pollution has always been a focus of attention for environmental researchers. In recent years, many scientists have found that phytoremediation aided by endophytes has high potential to remediate heavy metals owing to its low cost, effectiveness, environmental friendliness, and sustainability compared with physical and chemical methods. Indeed, the mechanism of interaction between endophytes, plants, and heavy metals in the soil is pivotal for plants to tolerate metal toxicity and thrive. In this review, we focus on the mechanism of how endophytic bacteria resist heavy metals, and the direct and indirect mechanisms employed by endophytic bacteria to promote the growth of plants and enhance phytoextraction and phytostabilization. Moreover, we also discuss the application of combinations of endophytic bacteria and plants that have been used to remediate heavy metal pollution. Finally, it is pointed out that although there have been many studies on phytoremediation systems that have been assisted by endophytes, large-scale field trials are important to deliver “real” results to evaluate and improve phytoremediation assisted with microorganisms in polluted natural environments.