In recent years, the concentrations and compositions of nutrients in the ocean have changed due to a variety of factors such as global warming, ocean acidification, and seawater eutrophication. The biomass and quality of macroalgae can be negatively affected by these nutrient dynamics. Recently, a strain of Gracilariopsis lemaneiformis with a curly branch (CB) phenotype, at the 2nd and 3rd generations, different from the normal branch (NB) phenotype, was discovered in cultivation field in China. The G. lemaneiformis cultivation industry has been negatively impacted by the malformation and coiling of this CB phenotype. In this study, seawater nutrient concentrations were measured and the CB part was investigated at the transcriptional level. The results showed that the concentrations and ratios of N and P varied at different sampling sites and times. There was a markedly negative correlation between the NO3--N, total-N, and PO43- concentration, and the degree of abnormality of this strain. Organic N biosynthesis, and the absorption and transport of inorganic N of the CB was down-regulated compared with NB. These preliminary findings suggest that the formation of the CB phenotype of G. lemaneiformis is related to a specific nutrient status in the cultivation field. This phenotypical variation in CB might be caused by a deficiency of N and P. These results provide important information on the response mechanisms and irregular branch formation of G. lemaneiformis under nutrient stress.