Fisheries management policies (FMPs) have been implemented in coastal countries to ensure a sustainable supply of seafood and the recovery of species diversity. Because of the depletion of fishery stocks, China has introduced a series of FMPs since 1995, including a seasonal fishing moratorium (SFM), a zero-growth strategy, and a minimum mesh size for fishing nets. Here, we built two mass balance models for 1997–2000 (M1997) and 2018–2019 (M2018) using Ecopath with Ecosim 6.6 to illustrate the interannual changes over the past two decades in the East China Sea (ECS). We then simulated two dynamic scenarios from 1997 to 2018, SFM (M2018SFM) and no SFM (M2018no-SFM), to test the role of the SFM under fishing pressure in the ECS. Ecopath showed that the ECS ecosystem is becoming more mature, although it is still unstable, featuring lower total primary production/total respiration, longer cycles, faster organic material circulation speed, and a higher omnivorous degree. This suggests a slow recovery for the ECS ecosystem in the past two decades. The biomass of fish in the ECS—especially the planktivores, dominated by small-sized Benthosema pterotum—significantly increased in M2018 versus M1997, but there were fewer medium- and large-sized fish. The keystone species switched from the planktivores/piscivores dominated by Decapterus maruadsi in M1997 to planktivores in M2018. Ecosim illustrated that the SFM has positive effects on fishery resources recovery, especially for commercial fishes (i.e., large yellow croakers and hairtails), as reflected by the significantly higher predicted biomass of fish in M2018SFM compared to M2018no-SFM and M1997, although the bioaccumulation was consumed by the intense fishing pressure after the SFM. However, the M2018SFM prediction for nektons was still lower than the actual value, especially for planktivores, which display a sharp increase in biomass. This should be partly attributable to the policy of the minimum mesh size (<5 cm was banned), which benefits B. pterotum due to its 3.5 cm maximum body size. Therefore, a series of FMPs, rather than only the SFM, functioned together in the ECS ecosystem. However, the mixed trophic impact indicated a negative impact if the fisheries were further developed. Fishery management in the ECS needs to be strengthened by extending the SFM and reducing fishing pressure after the SFM.