The differences between theoretical yield levels and farmers' actual yields define the yield gaps. Soybean is an important global commodity. Therefore, the present study was performed to investigate of the role of pod abnormality incidence on yield and yield components of soybean in Aliabad Katul, Golestan Province, Iran. During the growing season of soybean cultivation (2016-17), 120 farms were selected with a different range of conditions and crop management, soil characteristics, and planting date. Selected farms were at a maximum radius of 10 km from the meteorological station. Abnormality percent (dysfunction syndrome in the R3 stage of soybean growth), yield and yield components, and seed oil and protein contents were evaluated at the end of the experiment. The results of simple correlation coefficients showed that there was a significant and positive correlation between yield and yield components as well as seed oil content. According to the analysis of regression, there was a significant effect of abnormality percent (as the dependent variable) on yield and yield components (as independent variables) except number of pods with one seed and seed protein content. The improvement of morphological and yielding traits resulted in a reduction in the abnormality percent. In some cases, the damage of pod abnormality caused 30% reduction in grain yield. In general, among environmental and agronomic factors, the number of days with temperature higher than 25 °C at flowering stage (5 days before and 10 days after flowering = R3 growth stage of soybean) had a significantly positive correlation with the abnormality percent. It can be concluded that crop management such as suitable planting date, cultivation of tolerant genotype, irrigation management especially at flowering stage, nutrition management, and others, can reduce the severity of the abnormality percent.