To investigate the reasons for irregular and severe decreases in net ecosystem production (NEP) in a sod-cultured apple orchard for better understanding orchard carbon dynamics, CO₂ flux observation was conducted from April to November (2013 and 2014) using two sets of eddy covariance equipment on different towers that were 15 m apart. Special attention was paid to the effect of grass mowing, which was conducted ten times during the observation period. In the latter half of, or just after the grass mowing period, gross primary production (GPP) on fine (sunny) days decreased to 50%-73% of the level before the grass mowing nine out of ten times, whereas ecosystem respiration (RE) did not decrease or slightly increased. As a result, NEP (=GPP－RE) on fine days drastically diminished after every grass mowing event. Moreover, three other moderate NEP decreases were observed, in addition to mowing events. Two of these events, which occurred 9-10 days before apple flowering, were possibly caused by a temporal increase in the respiration of apple tree. The remaining event, which occurred immediately after the drought period, was possibly caused by the recovery of microorganism and root respirations. Moreover, in comparing the daily GPP trend in 2013 and 2014, it was apparent that meteorological conditions, such as low temperature from April to May or severe soil water deficiency and low solar radiation in the vigorous growth stage, also negatively affected the population photosynthesis of the orchard.