Accurate postmortem interval (PMI) estimation is critical for forensic investigations, aiding case classification and providing vital trial evidence. Early postmortem signs, such as body temperature and rigor mortis, are reliable for estimating PMI shortly after death. However, these indicators become less useful as decomposition progresses, making late-stage PMI estimation a significant challenge. Decomposition involves predictable microbial activity, which may serve as an objective criterion for PMI estimation. During decomposition, anaerobic microbes metabolize body tissues, producing gases and organic acids, leading to significant changes in skin and soil microbial communities. These shifts, especially the transition from anaerobic to aerobic microbiomes, can objectively segment decomposition into pre- and post-rupture stages according to rupture point. Microbial communities change markedly after death, with anaerobic bacteria dominating early stages and aerobic bacteria prevalent post-rupture. Different organs exhibit distinct microbial successions, providing valuable PMI insights. Alongside microbial changes, metabolic and volatile organic compound (VOC) profiles also shift, reflecting the body’s biochemical environment. Due to insufficient information, unimodal models could not comprehensively reflect the PMI, so a muti-modal model should be used to estimate the PMI. Machine learning (ML) offers promising methods for integrating these multimodal data sources, enabling more accurate PMI predictions. Despite challenges such as data quality and ethical considerations, developing human-specific multimodal databases and exploring microbial–insect interactions can significantly enhance PMI estimation accuracy, advancing forensic science.