Aerenchyma is a tissue formed via programmed cell death and lysis function for gas exchange in rice. Unlike roots, stem aerenchyma remains poorly characterized among different rice varieties and management conditions. This study investigated the morphological characteristics of stem aerenchyma among four rice varieties grown under contrasting water conditions (non-flooded and flooded) and N fertilizer applications (0 and 120 kg ha^–1). Rice plants were grown under a pot experiment in the greenhouse condition. The aerenchyma tissues of each rice variety were assessed in the early heading stage (98–105 days old from seed sowing). The stems were sectioned at the first node (~20–30 mm above the node) for 1 mm in thickness and aerenchyma tissues were quantified using Lugol’s solution staining under stereomicroscopy. The variation of aerenchyma tissues was found among different rice varieties. The varieties Pathum Thani 1 (PTT1) and Khao Dawk Mali 105 (KDML105) showed markedly higher aerenchyma traits (total cell area, average cell area, and percentage of formation) than the other varieties, particularly applying N fertilizer under flooded conditions. In PTT1, these traits increased by 1.57, 1.57, and 1.66 times, and 2.61, 2.54, and 1.63 times in KDML105, respectively, compared with the non-N. In contrast, the CMU K4 advanced line exhibited an increase in aerenchyma formation only when N fertilizer was applied under non-flooded conditions, with 1.23 times the increase relative to non-N, whereas San Patawng 1 (SPT1) showed morphological responses only in aerenchyma cell number, which increased by 1.23 times under non-flooded conditions when N fertilizer was applied. These results have demonstrated the variation in stem aerenchyma development among different rice varieties under varying management conditions, providing crucial physiological insights that may help explain differential gas exchange capacities among rice varieties under varying cultivation practices. The appropriate management may be a key solution for reducing aerenchyma density and consequently decreasing greenhouse gas emissions in rice cultivation. The knowledge gained from this study would be very useful in selecting rice varieties with different aerenchyma densities in breeding programs for developing high N use efficiency with low-greenhouse-gas-emission rice varieties.