The cereals and their products, which have been easily infected by fungi and contaminated with mycotoxins, are serious threat to both human and animals alike. And yet, detection of these unknown fungal infection and mycotoxins contaminates remains a great challenge. In this work, a holistic approach based on multiple characteristic structure fragments scans and high-resolution mass spectrometry (HRMS) was proposed for discovering unknown structural analogues of mycotoxins. The structural similarity of the same class of compounds provides a direction for the discovery and identification of unknown structural analogues of mycotoxins. The following steps were carried out: the fragmentation pathways of four types of mycotoxins were elucidated through comprehensive fragment analysis. By the combination of fragmentation pathways, the multiple characteristic structure fragments were screened out, with the common fragments were obtained by Veen diagram. Finally multiple characteristic structure fragments scans were carried out to find the unknown structural analogues of mycotoxins. The approach, first proposed by us, was proved to be effective in discovering and identifying 5 structural analogues of mycotoxins in real samples. It was proved to be a simple, fast and accurate method for early detection of fungal infection and mycotoxin contaminants, even for trace amounts of chemicals in complex matrix, and is of great significance to prevent hazardous substances infection from the food supply chains worldwide.