Soil Organic Matter (SOM) played a central role in many environmental and land use issues. In Taiwan, an island of 36,000 km² and traversed subtropical and tropical zones, the cultivation was intensive and chemical fertilizers were heavily used; consequently, more than 50% of arable land content SOM as low as less than 2%. The paddy-upland rotation and the application of various organic matters became more and more popular in its agricultural production. This study focused on using a simple model to develop suitable processes for evaluating the long term effects on carbon sequestration under the rotation systems with high organic matter input. The data were collected from field experiments of random block design, which had 7 treatments with 4 replicates as for 2 harvests a year and 7 years of continuous cultivations. Optimal parameter identifications for the dynamic model were done by genetic algorithm. The minimal years of data set was searched for the identification according to the fitness on simulating the total data bases of the field experiments of 7 years. Further more, the results also evaluated by the method of sensitivity analysis by checking the Root-Mean-Square Error (RMSE) between the observed data and the simulated results from a series of parameters perturbation. The minimal years of field data needed for finding the parameters to fit the variation of the 7 years experiments was found depending on the characteristics of applied organic matter. The parameters of the compost treatment, which had the obvious turnover trend, could be obtained by only using the data for as short as 2 years, while other treatments took 3 to 5 years. It meant that the variation of SOM could be governed by the model with limited years of data collection from the field systems. Long term predictions coincided with the fact that the highest accumulation, being near 3 times the initial content of SOM, came from the treatment of the input with hardly decomposable organic matter such as peat. The lowest increase was 1.2 times the initial content as was from the treatment with the smallest input of organic matter. System dynamic simulations showed that it took 20 to 40 years to reach equilibrium on SOM content for each treatment, implying that it took several decades to reach steady state of carbon sequestration as long as the land use and soil management were changed. The proposed simple model, once calibrated with a few years of field data, could be applied to evaluate the capacity and intensity of the long term effects of soil carbon sequestration in fields.