Globally, atmospheric nitrogen (N) deposition is rising, adversely impacting soil health, i.e., increasing soil acidity. While phosphorus (P) is the limiting element in the temperate environment and plays a key role in making the ecosystem more vulnerable to N-derived acidification. The impact of elevated N and P inputs on soil acidity and exchangeable base cations have been extensively studied; however, few studies have focused on these parameters, especially within various soil aggregate fractions in the temperate forest. In 2017, a field experiment was conducted under N and P additions with four soil aggregate fractions (>5 mm, 2–5 mm, 0.25–2 mm, and <0.25 mm) in two forests, i.e., the broad leave Korean pine forest (BKPF) and Korean pine plantation (KPP) in the Liangshui National Natural Reserves in Northeast China. Results showed that high NP addition decreases pH, base cations, Mg2+ Ca2+, and BS% and increases in Fe3+, Al3+, and E.A (effective acidity) in all four aggregate fractions, in descending order; overall concentration of the base cations is ranked as BKPF > KPP. Thus, soil acidification is primarily caused by a decrease in base cations, such as Ca2+ and Mg2+, and increase in exchangeable Fe3+ and Al3+ ions in large macro-aggregates and macro-aggregates, which leads to the depletion of soil nutrients. The initial pH value (5.69) in >5 mm soil aggregate was decreased to (5.4) under high fertilizer application, while a minimum value of 5.36 was observed in 0.25–2 mm aggregates under high fertilizer application. The same trend was observed in all aggregates because of decrease in base cations, which, in turn, affects the vitality and health of the forests.