The official establishment of China’s national parks marks a new stage in the construction of China’s ecological civilization system. National parks systematically protect the areas with the richest biodiversity and the most complete ecosystem processes in China. This is beneficial not only for China’s natural conservation work, but also for the world’s response to environmental issues, such as climate change. Based on remote sensing images of land use in the four periods 1990, 2000, 2010, and 2020, this study calculated the land use changes in each national park during the corresponding period. Using the Plus model LEAS module, the driving factors of land use change in the national parks were studied and explored. In addition, the study used the InVEST model carbon storage module, using remote sensing images from different periods and the corresponding carbon pools of each national park as the basic data for model operation, to obtain the carbon storage changes in each national park over the past 30 years. Based on the hotspot analysis function, the hotspot areas of carbon storage changes in the national parks in the past 30 years were determined. Consequently, based on the CARS module of the PLUS model, the carbon storage in Northeast Tiger and Leopard National Park in 2030 was estimated under different scenarios. Research suggested that, except for Sanjiangyuan National Park where grassland is the main land use type, the other four national parks are all dominated by forests, and the expansion and changes in the main land use types were due to human activities. In the past 30 years, the carbon storage in China’s national park ecosystem has mainly shown a trend of first increasing and then gradually decreasing. Based on the changes in carbon storage in the national park, restoration scenarios were simulated for the core protected and generally controlled areas of Northeast Tiger and Leopard National Park. Under the ideal scenario, the highest value of carbon storage would be achieved by 2030, which would be 7,468,250 t higher than that in 2020. The present study provides a reference for the regional management of China’s national parks and further confirms that the implementation of the national park system can enhance China’s ability to achieve carbon peaking and neutrality goals.