Compared to extensive studies reporting the aluminum (Al) toxicity to terrestrial plants and freshwater organisms, very little is known about how marine phytoplankton responds to Al in the field. Here we report the marine phytoplankton responses to Al enrichment in the South China Sea (SCS) using on-deck bottle incubation experiments during eight cruises from May 2010 to November 2013. Generally, Al addition alone enhanced the growth of diatom and Trichodesmium, and nitrogen fixation, but it inhibited the growth of dinoflagellates and Synechococcus. Nevertheless, Al addition alone did not influence the chlorophyll a concentration of the entire phytoplankton assemblages. By adding nitrate and phosphate simultaneously, Al enrichment led to substantial increases in chlorophyll a concentration (especially that of the picophytoplankton < 3 μm), and cell abundances of diatom and photosynthetic picoeukaryotes. These results indicate varied responses of phytoplankton in different size fractions and taxonomic groups to Al enrichment. Further, by simultaneously adding different macronutrients and/or sufficient trace metals including iron, we found that the phytoplankton responses to Al enrichment were relevant to nutrients coexisting in the environment. Al enrichment may give some phytoplankton a competitive edge over using nutrients, especially the limited ones. The possible influences of Al on the competitors and grazers (predators) of some phytoplankton might indirectly contribute to the positive responses of the phytoplankton to Al enrichment. Our results indicate that Al may influence marine carbon cycle by impacting phytoplankton growth and structure in natural seawater.