Currently, impacts of rapid cropland reclamation and its intense structural changes in internal paddy-upland on ecosystem service are insufficient in Sanjiang Plain, China. Further, land management systems of Sanjiang Plain consist of state-owned and private farms; however, exploring the impact of different land management systems on “land use–landscape–ecosystem service” is still lacking. To reveal this issue, the integrated methodology of “land dynamic tracking–landscape index–improved ecosystem service assessment” was established. Results are displayed below: From 1990 to 2020, land use was featured by decreases in forest (−3308.62 km2), grassland (−6030.86 km2), waters (−475.81 km2), and unused land (−3037.27 km2), with a slight increase in constructed land (+403.25 km2) and a rapid increase in cropland (+12,447.56 km2). Although nearly equal increments of cropland on state-owned and private farms (i.e., 6156.70 km2 vs. 6290.86 km2) were monitored, different cropland structure changes were still revealed, namely a drastic expansion of paddy fields (13,788.32 km2) and an acute decrease in upland crops (−7631.62 km2) on state-owned farms, but both a slight increments in paddy fields (5920.08 km2) and upland crops (370.78 km2) on private farms. For landscape, private farms were more fragmented (SHDI = +0.63%), causing a decrease in aggregation (AI = −0.56%) and a more complex shape (LSI = +23.3%), by contrast, state-owned farms displayed an increased integrity (SHDI = −9.88%), along with an increase in aggregation (AI = +0.43%) and simplified shape (LSI = −13.30%). Evaluated ecosystem service value changed from 338.62 to 296.25 billion yuan from 1990 to 2020, a loss rate of 12.58% in Sanjiang Plain. Then, a new finding showed a higher loss rate on state-owned than private farms (i.e., 30.15% vs. only 6.18%). This study revealed differentiated processes of “land use–landscape–ecosystem service” in different land management system regions in China, providing new findings in the fields of land management system, ecological landscape, and environment.