The Arctic Ocean has been experiencing the rapid climate changes such as warming and sea ice melt. Further, the large area of sea ice retreat enhance ocean uptake of CO2. We conducted two shipboard experiments in September 2015 and 2016 to examine the effects of temperature, CO2, and salinity on phytoplankton dynamics to better understand the impacts of climate changes on the Arctic ecosystem. Two temperature (Control and 5°C above the Control), two CO2 (Control and 300/450 μatm above the Control), and two salinity (Control and 1.4 below the Control) conditions were fully factorially manipulated in eight treatments. Higher temperature enhanced almost all phytoplankton traits, whereas the experiment in 2015 demonstrated that diatom diversity decreased due to the replacement of chain-forming Thalassiosira spp. by solitary Cylindrotheca closterium. Higher CO2 levels significantly increased the growth of small-sized phytoplankton (<10 μm) in both years. Decreased salinity had marginal effects but significantly increased the growth of small-sided phytoplankton in terms of chl-a in 2015. This study demonstrates that the change in phytoplankton community structure in the shelf edge region of the Chukchi Sea in the western Arctic Ocean under multiple environmental perturbations are likely to lead to decreases in the efficiency of the biological carbon pump, trophic transfer and food supply for benthos.