Aspergillus is a fungal genus widely studied all over the world because some species are known allergens and opportunistic human pathogens. The dynamic growth of Aspergillus is a prerequisite for establishing safe storage time of orange peel. In this paper, high‐throughput sequencing technique was used for the first time to analyze the diversity and structure of fungi in the same batch of samples at different periods of time, and 20 batches of fresh orange peel and 56 batches of dried peel were verified. Results shown that the orange peel gradually began to grow Aspergillus fungal after storing for 240 days, and the abundance became maximum at 270 days and then decreased. These results suggest the safe storage time should be from January to August. And orange peel should be dried in August to prevent rapid propagation or metabolic toxicity production of Aspergillus fungi.