Soil aggregation in forest ecosystem is considered as a significant physical process mainly influenced by manure, fertilizers or combination. This aggregation may directly alter the soil nutrient and their fractions in soil. So, soil samples were collected from two types of forests i.e. Natural Korean pine forests (NKPF) and Korean pine plantation (KPP) in order to know the quantities of organic and inorganic Phosphorus (P) amounts in different aggregate sizes viz. >5 mm, 2–5 mm, 0.25–2 mm, <0.25 mm under forest litter and synthetic fertilizer application below the treatments as undisturbed soil (CK), removed litter (RL), altered litter (AL) while the fertilizer treatments were as control; C: (No added N and P,), L: low (5 g N m−2a−1+ 5 g P m−2a−1), M: medium (15 g N m−2a−1+ 10 g P m−2a−1) and H: high concentration (30 g N m−2a−1+ 20 g P m−2a−1), respectively. The results showed that H2O-Pi, NaHCO3-Pi, Residual Pi, SOC were highest retained in larger soil aggregates (>5 mm) and decreased with the decreasing aggregate size, while other variables, i.e., NaOH-Pi, NaHCO3-Po, pH and T-N were not affected in aggregate size. H2O-Pi (48 ppm), NaHCO3-Pi (68 ppm), NaHCO3-Po (80 ppm), NaOH-Po (623 ppm), HCL-Po (67 ppm), SOC (20.36 ± 1.6) was estimated in medium fertilizer treatment. PCA analysis showed that spread/variance of data points on F1 (62.90%) is more than spread/variance of data points on F2 (57.74%) in NKPF and KPP, respectively, while correlation matrix showed high correlation between H2O-Pi and NaOH-Pi (0.63) and H2O-Pi and NaHCO3-Pi (0.63) while a strong negative correlation was present between Res-Pi and Po (−0.61). Moreover, litter inputs increased the organic-P fractions in soil particularly at medium treatment.