Drought is considered one of the devastating natural disasters worldwide. In the context of global climate change, the frequency and intensity of drought have increased, thereby affecting terrestrial ecosystems. To date, the interactions between ecosystem change and drought, especially their mutual lag and cumulative effects is unclear. The Songnen Plain in northeastern China is one of the three major black soil areas in the world and is highly sensitive to global change. Herein, to quantify the interaction between drought and ecosystem function changes in the Songnen Plain, integrating with time-series moderate resolution imaging spectroradiometer (MODIS), leaf area Index (LAI), evapotranspiration (ET), and gross primary productivity (GPP) data, we calculated the standardized precipitation and evapotranspiration index (SPEI) based on the meteorological data, diagnosed the causal relationship between SPEI and the ecosystem function indicators i.e., LAI, ET, and GPP, and analyzed the time-lag and cumulative effects between the degree of drought and three ecosystem function indicators using impulse response analysis. The results showed that the trend of SPEI (2000–2020) was positive in the Songnen Plain, indicating that the drought extent had eased towards wetness. LAI showed insignificant changes (taking up 88.34% of the total area), except for the decrease in LAI found in some forestland and grassland, accounting for 9.43%. The pixels showing a positive trend of ET and GPP occupied 24.86% and 54.94%, respectively. The numbers of pixels with Granger causality between LAI and SPEI (32.31%), SPEI and GPP (52.8%) were greater at the significance 0.05 level. Impulse responses between each variable pair were stronger mainly between the 6th and 8th months, but differed significantly between vegetation types. Grassland and cropland were more susceptible to drought than forest. The cumulative impulse response coefficients values indicated that the mutual impacts between all variables were mainly positive. The increased wetness positively contributed to ecosystem function, and in turn enhanced ecosystem function improved regional drought conditions to some extent. However, in the northeastern forest areas, the SPEI showed a significant negative response to increased ET and GPP, suggesting that the improved physiological functions of forest might lead to regional drought. There were regional differences in the interaction between drought conditions and ecosystem function in the Songnen Plain over the past 21 years.