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To explore the effect of storage conditions on the freshness of fishmeal, the acid value (AV), volatile basic nitrogen (VBN), and pH value were used as freshness evaluation indexes to explore the changes in freshness during storage and the influence of mold count on these indexes. The effects of storage temperature and relative humidity (RH) on AV, VBN, pH value, and mold count were studied using a single-factor test, and grey relation analysis (GRA) was used to assess the association between mold count and freshness indexes. The appropriate storage conditions were determined using the technique for order preference by similarity to ideal solution (TOPSIS) method, which provides theoretical support for fishmeal storage. The results showed that the AV increased during the storage of fishmeal, while the VBN and pH value decreased; the pH value tended to be stable in the later storage stage. The VBN and pH values could not be used as evaluation indexes in the early stage of deterioration. Higher storage temperature was conducive to the storage of fishmeal, but higher RH was not. The results of the GRA showed that the mold count was correlated with each freshness index. The correlation between mold count and VBN was the largest, followed by AV, and the correlation with pH value was the smallest. The TOPSIS method finally determined the suitable storage conditions for fishmeal to be around 25 °C for storage temperature and 60% for RH. The results serve as a future reference for the storage of fishmeal.