This study was conducted in Mt. Makiling Forest Reserve (MFR), Luzon, Philippines to compare the carbon cycle pattern according to regeneration method by analyzing the carbon storage and flux of a large leafed mahogany (Swietenia macrophylla King) plantation and a   secondary natural forest. The total carbon storage in aboveground  biomass, litter layer and soil of the secondary forest stand was 313.12  Mg C/ha, which was 1.7 times larger than the carbon storage of the large leafed mahogany plantation (185.28 Mg C/ha). The stocks of carbon in the aboveground biomass and soil were higher in the  secondary forest stand than in the large leafed mahogany plantation. The carbon content in litter layer was higher in the large leafed mahogany plantation than in the secondary forest stand. The soil carbon storage in the secondary forest stand and large leafed mahogany plantation at a depth from 0~60 cm was 82.25 and 69.04 Mg C/ha, respectively. The higher soil carbon stock in the secondary forest stand was due to the soil carbon stock in the 0~20 cm depth. The litter production in the dry season was higher in the large leafed mahogany plantation (4.23Mg C/ha) than in the secondary forest  stand (2.90 Mg C/ha) because of the high weight of the fruit. The litter  production in the wet season was higher in the secondary forest stand than in the large leafed mahogany plantation because of the high  mass of leaves and branches.