Lake ice is an essential and integral part of the cryosphere and freshwater systems. The formation of lake ice affects the physical, hydrological, and biological conditions of ecological systems. Global warming may contribute to even shorter periods of ice cover in the lakes of the Frigid Zone, which adversely affects the growth of phytoplankton and primary productivity. This study was conducted for the purpose of evaluating the growth of phytoplankton and factors involved, in 28 ice-covered lakes across the Songnen Plain, in the Northeast of China, to understand how they take part in the whole-ecosystem functioning. A total of 1026 water samples were collected in April, September, and January during the period 2014–2018. In the frozen period, the concentration levels of dissolved organic carbon (DOC), total nitrogen (TN), and total phosphorus (TP) were all comparable with the spring and autumn. Despite the limited light availability and low temperature, the phytoplankton survived in sub-ice waters during winter with a low concentration of chlorophyll a (Chla). Its average concentration was positively correlated with the concentration observed in the previous autumn (r_p = 0.563, p < 0.01). According to the regression tree analysis, during the winter period, Chla was mainly related to the concentration of TN in sub-ice water (TN_water) and with the difference of concentration of TP between water and ice (TP_cd). Furthermore, either in ice or in sub-ice water, the concentration of Chla was also significantly affected by total suspended matter (TSM) (p < 0.05). The levels of TN_water, TP_cd, and TSM could explain the 77.8% of the variance in the concentration of Chla during winter with contributions in the ranges of 25.5%–35.0%, 9.2%–11.3%, and 21.5%–34.0%, respectively (p < 0.05). This research substantially contributes to comprehending how the existing conditions under-ice affect the whole ecosystem when the ice cover is reduced lakes or rivers.