Microbial toxins generated by bacteria, fungi and algae cause serious food-safety problems due to the frequent contamination of foodstuffs and their poisonous nature. Becoming acquainted with the contamination condition of foodstuffs is highly dependent on developing sensitive, specific, and accurate methods for targeting microbial toxins. Aptamers, obtained from systematic evolution of ligands by exponential enrichment (SELEX), have significant advantages for microbial toxin analysis, such as small size, reproducible chemical synthesis, and modification, as well as high binding affinity, specificity, and stability. Besides, aptamers have a predictable structure and can be tailored using biomolecular tools (e.g., ligase, endonuclease, exonuclease, polymerase, and so on), which is conducive to the development of flexible and variable amplification methods. Recent studies revealed that the combination of aptamers and noble metal nanomaterials offers unprecedented opportunities for microbial toxin detection. Noble metal nanomaterials with outstanding physical and chemical properties facilitate the detection process and improve the sensitivity and specificity. In this review, we discuss current progress in the development of various noble metal nanomaterial-based aptasensors for microbial toxin detection. These noble metal nanomaterials include gold nanoparticles, gold nanorods, gold nanoclusters, silver nanoparticles, silver nanoclusters, and bimetallic nanomaterials. Aptasensors based on noble metal nanomaterials exhibiting high selectivity and sensitivity represent a promising tool for microbial toxin detection.