Golden mussel (Limnoperna fortunei) and zebra mussel (Dreissena polymorpha) are representative species of invasive mussels in freshwater system. Benefiting from molecular biological technology development, the environmental DNA (eDNA) technology has been applied for rapid detection of mussel invasions. However, the sensitivity and quantitative efficiency of eDNA technology are significantly affected by abiotic and biotic environmental parameters when we undertake monitoring of the invasive species during their introduction, colonization, and diffusion processes. In this review, we systematically searched for publications about monitoring of mussel invasions using eDNA technology and analyzed key factors affecting the efficiency and accuracy of eDNA monitoring, including sampling scheme, primer design, quantitative analysis, quality assurance, and portable instrumentation. Based on the summary above, we explored the advantages and limitations of eDNA technology in the invasive mussel monitoring and proposed potential improvements of the technology for future application.