The traditional water quality regulations could not break up thermocline and inhibit macroalgae growth, which result in poor water quality and Apostichopus japonicus growing poorly and even death. Jet water mixing (JWM) can break up thermocline and inhibit the growth of macroalgae. To study the purification efficiency and mechanism of JWM, the primary productivity in the ponds with a jet water mixer (JWM), a submerged aerator (SA) or without any artificial mixing (control) were studied. The results showed that the annual average primary productivity and P/R values of the pond with JWM were the highest, followed by SA pond, and the lowest in the pond without any artificial mixing (control). The mean annual primary productivity in the ponds with JWM, SA and Control pond were 6.22±0.54, 5.37±0.60 and 4.69±0.53 gO₂/(m²·d), respectively. The primary productivity in the ponds decreased with the depth of water. There was no significant difference in primary productivity between 30-50 cm water layer and 50-100 cm water layer in JWM pond, while there was significant difference between the SA pond and Control pond (P<0.05). In addition, the primary productivity of the water layer of 50-150 cm in JWM pond was significantly higher than that of the SA and control pond (p<0.05) from June to September. Conclusion: compared with SA facility, JWM can improve significantly the primary productivity of the lower water layer, which can significantly improve the total primary productivity of the pond and facilitate the rapid circulation of the pond substances.