Lake ecosystems are impacted by anthropogenic disturbances and have become vulnerable worldwide. Highly disturbed lake ecosystems are not well understood due to the lack of data on changes in the structures and functions of ecosystems. In this paper, we focus on Lake Baiyangdian (BYDL), the largest shallow lake in North China. Following the establishment of the Xiong’an New Area (XNA) in 2017, concerted efforts to restore BYDL’s aquatic environment have been undertaken, which has led to significant changes in the structures and functions of the ecosystems. We evaluated the biomass dynamics of main biological communities and detected the regime shifts of environmental factors in BYDL from 2016 to 2023. Further, we constructed a food web model for the BYDL ecosystem in 2023 by using Ecopath with Ecosim (EwE) and made a comparison with the reported results in 2018. The results showed significant changes in the ecosystem structure of BYDL over the last 6 years. In 2023, the submerged macrophytes biomass in the system increased by 4.2 times compared to 2018, leading to an increase in total system throughput. We found that BYDL changed from an algal-type lake to a macrophyte-dominated lake. In addition, we found TN, NH4+-N, and CODMn were significantly decreased in BYDL during the restoration. TN and NH4+-N had a change point in approximately 2021, indicating that a regime shift had occurred during restoration. Overall, the BYDL ecosystem was in an immature but developing state, as indicated by ecological network analysis indicators. Nutrient-loading reduction, hydrological regulation, and rational biomanipulation may be the potential driving factors of change in the BYDL ecosystem. We strongly recommend the timely harvesting of submerged macrophytes, the proliferation and release of herbivorous fishes, and the assessment of the ecological capacity of carnivorous fishes in the future ecological restoration of BYDL.