Simulation experiments were conducted to study the response of phytoplankton biomass and community composition to the influence of polymetallic nodules and sediment at four stations in the western Pacific in 2021. Chlorophyll a, pico-phytoplankton cell abundance, and metal concentration was measured before and after 24 h of deck incubation. The results showed that there were three different patterns of response, including restrain, stimulate, and unaffected patterns. The restrain pattern appeared in the filtered treatments at station Incub. 01, and the stimulated pattern appeared in the unfiltered treatments at station Incub. 02. The response of the phytoplankton was not detectable at stations Incub. 03 and 04. Regardless, the positive or negative response was contributed by the dominant pico-phytoplankton group-Prochlorococcus, and with slight variation in Synechococcus. The concentration of manganese varied among the treatments, as compared to iron and other metals. The factors affecting the growth of the phytoplankton in the study were in metal concentrations and turbidity. The phytoplankton biomass baseline may also have played an important role: the lower the biomass, the higher the growth rate. This study proved that deep-sea polymetallic nodule mining will have a specific impact on surface phytoplankton biomass, but the turbidity and particles retention time could be important factors in mitigating the extent of impact.