The Hailar River is an important river, which plays an extremely important role in maintaining the ecological balance in the Inner Mongolia Autonomous Region. This study selects the lower reaches of the Hailar River as the research object (hereinafter referred to as the Hailar River). Based on remote sensing, climate, and hydrological data, we analyze the floodplain wetlands in the lower reaches of the Hailar River in response to climate change by the inundation frequency model analysis. The results show that the climate in the Hailar River area has presented a trend of dry and cold changes in the past 30 years, with an averagely annual rainfall of 356.45 mm, an averagely annual decrease of 11.64 mm, and a multi-year average temperature of -0.2℃, an averagely annual decrease of 0.01℃; The annual runoff shows a decreasing trend, with an average annual decrease of 2.05×108 m³; The Hailar River area belongs to the northeastern permafrost region. As the temperature drops and the frozen soil increases, the snowmelt recharge runoff decreases in May, which has an impact on the Hailar River runoff. The rainfall from June to October directly recharges the runoff, and as rainfall decreases, runoff reduction; The submerged areas under each submergence frequency are affected by runoff changes to different degrees. The extremely high submerged frequency area greater than 80% is the least affected by runoff, because this area is located on both sides of the main channel, and the 0-20% extremely low frequency area is most affected by runoff changes. Because this area is far away from the main river, the decrease in temperature of the Hailar River leads to the increase of the freezing time in the Hailar River area, inhibiting the generation of runoff in May, and the reduction of rainfall, resulting in the delay of runoff from June to October, affecting the water supply of the river to the wetland of the floodplain. Insufficient water supply in the river will cause to reduce the horizontal connection between the floodplain and the river, thereby reducing the number of times that the river overflows out of the channel, reducing the floodplain wetland inundation frequency, affecting the floodplain wetland inundation status, so as to serve the ecosystem in the extremely low inundation frequency area below 20% on both sides of the river bank. The function produces an inhibitory effect. The results can provide theoretical support for the Hailar River's ecological environment protection and water resources development and utilization.