The trophic status assessment of lakes in different lake regions may provide important and fundamental information for lake trophic state classification and eutrophication control. In this study, a region-specific lake eutrophication assessment standard was established through a frequency distribution method based on chlorophyll-a concentration. The assessment standards under the oligotrophic state for lakes in the Eastern plain, Yungui Plateau, Northeast Plain and Mountain Mongolia-Xinjiang regions are total phosphorus of 0.068, 0.005, 0.011, 0.005 mg/L; total nitrogen of 1.00, 0.16, 0.37, 0.60 mg/L; Secchi depth of 0.60, 8.00, 1.55, 3.00 m; and CODMn of 2.24, 1.00, 5.11, 4.00 mg/L, respectively. Moreover, a region-specific comprehensive trophic level index was developed to provide an understandable assessment method for the public. The results indicated that the frequency distribution analysis based on chlorophyll-a combined with trophic level index provided a useful metric for the assessment of the lake trophic status. In addition, the difference of eutrophication assessment standards in different lake regions was analyzed, which suggested that the sensitivities of algae to nutrients and the assessment standard of trophic status possessed significant regional differences for the four lake ecoregions. Lake eutrophication assessment standards would contribute to maximizing the effectiveness of future management strategies, to control and minimize lake eutrophication problems.