In aquatic products companies, saccharides and phosphates are often used to impregnate products to improve their quality. Insignificant impregnation effect is a main problem met in the impregnation process. The effect of ultrasonic-assisted impregnation on the storage quality of snakehead fish fillets at −18 °C was studied. For all samples, such parameters as water holding capacity, pH value, salt-soluble protein content, whiteness and cooking loss rate were examined periodically. Furthermore, the changes of moisture distribution and migration in snakehead fish fillets during storage were investigated using low-field nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI). The results demonstrated that ultrasonic-assisted impregnation showed better anti-freeze and water holding capacity effects than that of cryoprotectant impregnation alone. Therefore, ultrasonic treatment could be used as an effective way to improve the quality of snakehead fish fillets during the frozen process. This study could provide a broad application prospect in aquatic product processing industry.