Effect of land use change from paddy rice cultivation to upland crop cultivation on soil carbon budget (SCB) was studied by comparing three types of cropping system (single cropping of paddy rice (PR), single cropping of upland rice (UR) and double cropping of soybean and wheat (SW)) in an experimental field having the same history as consecutively cultivated paddy rice fields. The carbon dioxide (CO2) and methane (CH4) fluxes from the fields were measured continuously over 2.5 years with an automated flux monitoring system. Atmospheric CO2 was significantly absorbed during the growth periods of different crops, including all the summer crops and winter wheat. The amounts of absorbed CO2 during the summer crop growth period were highest in the PR plots and lowest in the UR plots. On the other hand, CO2 emission was observed during the fallow period. In addition, a significantly high peak and the subsequent gradual decrease in CO2 emission were observed after plowing the fields in autumn. Significant CH4 emission was found in only the PR plots during the submerged period. With consideration of gas flux data and the amount of carbon supplied and removed by agricultural management practices such as straw incorporation and crop harvest, the SCB in the croplands was estimated. The soil carbon budgets of the PR plots were positive (79–137gCm−2y−1), which indicates the accumulation of carbon in the soil. On the other hand, those of the UR and SW plots were negative (−343 to −275gCm−2y−1 and −361 to −256gCm−2season−1, respectively), which indicates significant carbon loss from the soil. The contribution of CH4 emission to SCB was small compared with that of CO2 dynamics. Significant differences in the carbon content of the top soil between the plots were also found after the experiment, consistent with the above SCB result. The results indicate that land use change from paddy rice cultivation to upland crop cultivation causes significant loss of carbon from cropland soil.