An in-depth understanding of the dominant factors controlling soil respiration is important to accurately estimate carbon cycling in forest ecosystems. However, information on variations in soil respiration at different soil depths and the influencing factors in forest is limited. This study examined the variations in soil respiration at two soil depths (0–10 and 10–20 cm) as well as the effects of soil temperature, soil water content, litter removal, and root cutting on soil respiration in three typical forest types (i.e., Pinus tabulaeformis Carrière, Platycladus orientalis (L.) Franco, and Quercus variabilis Bl.) in the mountainous area of north China from March 2013 to October 2014. The obtained results show that soil respiration exhibited strong seasonal variation and decreased with soil depth. Soil respiration was exponentially correlated to soil temperature, and soil respiration increased with soil water content until reaching threshold values (19.97% for P. tabulaeformis, 16.65% for P. orientalis, and 16.90% for Q. variabilis), followed by a decrease. Furthermore, interactions of soil temperature and water content significantly affected soil respiration at different soil depths of forest types, accounting for 68.9% to 82.6% of the seasonal variation in soil respiration. In addition to soil temperature and water content, aboveground litter and plant roots affected soil respiration differently. In the three forest types, soil respiration at two soil depths decreased by 22.97% to 29.76% after litter removal, and by 44.84% to 53.76% after root cutting. The differences in soil respiration reduction between the two soil depths are largely attributed to variations in substrate availability (e.g., soil organic content) and soil carbon input (e.g., litter and fine root biomass). The obtained findings indicate that soil respiration varies at different soil depths, and suggest that in addition to soil temperature and water content, soil carbon input and dissolved organic substances may exert a strong effect on forest soil respiration.