Recirculating aquaculture systems (RASs) are a sustainable aquaculture model strongly advocated by Chinese government. Earthy-musty is an important factor affecting the economic benefit and food safety of RAS. Geosmin (GSM) and 2-methylisobornyl (2-MIB) are the main substances that produce earthy-musty, which have a low human sensory threshold. Their accumulation leads to the earthy-musty of aquatic products, which greatly reduces the taste and economic value of these products and also threatens the sustainable development of aquaculture in China. GSM and 2-MIB are predominantly produced by heterotrophic prokaryotes in RASs. The production of these odorants is closely related to environmental factors, water quality parameters, and microbial community composition and is regulated by functional enzymes. Since the water exchange rate of RASs is only 5%, the current earthy-musty substances (EMS) treatment technology is not suitable for this system, and a cost-effective EMS removal technology is urgently needed. We put specific emphasis on the removal of EMS in RAS farms. Finally, we predict the challenges faced by EMS purification in RASs under the “comprehensive development of aquaculture” guideline by the Chinese government. In this review, first, we discuss the current GSM and 2-MIB generation mechanism in RASs, and then, based on the characteristics of RASs, we describe the transformation rules and removal methods of EMS in water systems and aquatic products, respectively. Finally, a new idea for removing EMS in RASs is proposed; that is, lipid adsorbents cooperate with functional microflora to remove EMS. This review provides scientific basis for eliminating the off-flavor of aquatic products, providing technical support for the promotion of RASs.