The impact of excessive rainfall or waterlogging on maize growth and yield have been widely studied, but the effects of planting density and N management under waterlogging remain unknown. We observed the changes in maize yield caused by excessive rainfall via a short-term experiment (2017 to present) in Changchun (125°14.231′–125°14.914′ E, 43°56.603′–43°57.274′ N), China. The experiment was conducted at four planting densities (45,000, 60,000, 75,000 and 90,000 plants/ha) and three nitrogen (N) rates (120, 180, and 240 kg/ha). The objective was to explore the effect of excessive precipitation on maize yield through changes in maize growing conditions, and the uptake, allocation, and utilization of N under different planting densities and N rates from 2019 to 2022. The precipitation during the whole growth period of maize in 2019 (542.9 mm) and 2020 (560.0 mm) was normal, while it was excessive in 2021 (829.10 mm) and 2022 (953.56 mm), especially during the vegetative stage from V12 to VT (355.60–482.10 mm). Excessive rainfall negatively affected the growth, photosynthetic characteristics (Pn: −20.00 %, SPAD: −50.50 %), absorption (−56.86 %), distribution (−15.83 %), N utilization efficiency (NUE: −29.69 %), and grain yield (−44.67 %) of maize. Our results indicate that yield loss was minimized (−22.88 %) when the planting density was appropriately reduced (from 75,000 to 60,000 plants/ha) and the N rate was increased from 180 to 240 kg/ha. The effect of different waterlogging durations on yield exhibited a significantly negative linear relation (R2 > 0.80). This study revealed the physiological mechanism of the sustained effects of excessive rainfall on maize growth and yield. Waterlogging significantly affected the SPAD of maize (p < 0.01, R2 = 0.04), resulting in insufficient kernel N content (p < 0.001, R2 = 0.16) and decreased NUE (p < 0.001, R2 = 0.48). These factors significantly affected yield and exerted a significant negative correlation with planting density (p < 0.05). Our findings improved understanding of planting density and N management for growth and yield of maize under excessive rainfall conditions in mid-high latitude agriculture areas of the world.