Prepared aquatic products refer to ready-to-eat, heated, ready-to-cook, and paired food derived from marine products, which are growing as attractive convenience food. Flavor is a vital factor for consumers in choosing prepared aquatic products. Suitable packaging materials and methods are the crucial pathways used to maintain the flavor and control the off-flavor of prepared aquatic products. Compared to vacuum packaging and modified atmosphere packaging, innovative packaging, including biodegradable, edible, active, and intelligent packaging, has received attention due to the potential advantages of flavor regulation. The mechanism of flavor change in package-associated prepared aquatic products is surveyed in this paper according to the reaction of lipids, proteins, microorganisms, and enzymes. Further, the effects of innovative packaging materials and methods on the flavor regulation of prepared aquatic products are summarized under the investigation of typical packaging. Moreover, prospects for innovative packaging materials and methods for flavor regulation in prepared aquatic products are proposed. This review provides references and bases for developing innovative packaging that maintain the flavor and wipes off-flavor.