So far, the least is known about the D-region ionosphere out of the entire ionosphere due to the lack of a conventional detecting method and continuous data accumulation. Medium frequency (MF) radar is an important conventional tool for understanding the D-region ionosphere by measuring the electron density (Ne) within the height range of 60–90 km. To investigate the statistical variation of the D-region, especially at the mid-low latitude area, this study presents the statistical variations in the D-region Ne with the solar zenith angle (SZA), season, and altitude observed by Kunming MF radar (25.6° N, 103.8° E) under low solar activity (2008–2009). The diurnal variation of Ne behaves like typical diurnal changes, which are closely consistent with the SZA. The outstanding feature, the diurnal asymmetry phenomenon, significantly appears in different seasons and at different altitudes. The Ne has obvious semi-annual characteristics, and is larger in summer and fall and the smallest in winter. Compared to other seasons, the variation in the Ne with altitude is the most stable in summer. Due to the impacts of the highest SZA, the value of Ne in winter is the smallest, with a maximum value of less than 300 electrons/cm3, and the largest in summer and fall, with a maximum of 472 electrons/cm3. Particularly, the peaks of Ne above 76 km do not always appear at the time when the SZA is the smallest (at noon). Both the simulations by the International Reference Ionosphere (IRI2016) and observations using MF radar present a strong positive correlation with solar radiation. Meanwhile, it cannot be ignored that there were still large differences between the simulations and observations. To quantitatively analyze the differences between the observations and simulations, the observed value was subtracted from the simulated value. The results show that the maximum value between them was up to 350 electrons/cm3, and the minimum difference appeared at around 72 km, with a value less than 100 electrons/cm3. However, below 66 km, the observations were larger than the simulations, which were, on the contrary, above 76 km.