Over the past two decades, the environmental characteristics of the northern East China Sea (NECS) that make it a crucial spawning ground for commercially significant species have faced substantial impacts due to climate change. Protein (PRT) within phytoplankton, serving as a nitrogen-rich food for organisms of higher trophic levels, is a sensitive indicator to environmental shifts. This study aims to develop a regional PRT algorithm to characterize spatial and temporal variations in the NECS from 2012 to 2022. Employing switching chlorophyll-a and particulate organic nitrogen algorithms, the developed regional PRT algorithm demonstrates enhanced accuracy. Satellite-estimated PRT concentrations, utilizing data from the Visible Infrared Imaging Radiometer Suite (VIIRS), generally align with the 1:1 line when compared to in situ data. Seasonal patterns and spatial distributions of PRT in both the western and eastern parts of the NECS from 2012 to 2022 were discerned, revealing notable differences in the spatial distribution and major controlling factors between these two areas. In conclusion, the regional PRT algorithm significantly improves estimation precision, advancing our understanding of PRT dynamics in the NECS concerning PRT concentration and environmental changes. This research underscores the importance of tailored algorithms in elucidating the intricate relationships between environmental variables and PRT variations in the NECS.