A non-targeted metabolomics technique was employed to investigate the dynamic metabolite changes of scallop (Patinopecten yessoensis) adductor muscle (SAM) and scallop mantle (SM) during the early (E), middle (M), and late (L) harvest period from June to July. Many more metabolites were identified from SM (831) than from SAM (231), and 24 and 12 significantly differential metabolites were screened, respectively. Organic acids and derivatives, lipids and lipid-like molecules, and organoheterocyclic compounds were the primary metabolite classes in both SAM and SM. In SAM, the levels of most altered metabolites, such as butyryl carnitine, (±)8-HEPE, 14(S)-HDHA, l-Kynurenine, and l-(−)-Methionine), decreased with the extended harvest time, whereas pipecolic acid and oleamide increased. Conversely, in SM, linoleamide, oleamide, dimethyl citrate, kynurenine, and pipecolic acid declined, while 5,6-Dihydrothymidine, dimethylsulfoniopropionate, and 13(S)-HOTrE increased with a longer harvest time. Pipecolic acid, exhibiting an obvious up-regulated response during the whole harvest period, was found to be the sole differential metabolite shared by SAM and SM. Annotation analysis showed that five metabolites were respectively identified in SAM and SM, and these metabolites were separately related to five metabolic pathways with slight differences among the two tissues. Amino acid metabolism/degradation and fatty acid metabolism were the primary pathways. These findings could provide new insights into the dynamic quality changes of scallops during the harvest period and may play a potential guiding role in the aquaculture and harvest of scallops.