Knot-related defects are important criteria for timber grading of valuable tree species. Clear-wood production through pruning has been an important issue in silviculture and forest management. In this study, knot attributes, branch occlusion and discoloration under natural and artificial pruning were investigated in a 10-year-old Betula alnoides plantation to determine the effectiveness of artificial pruning in mitigating knot-related defects. The dataset contained 270 occluded branches sampled from 30 artificially-pruned trees and 284 from 30 trees under natural pruning. Linear and generalized linear mixed-effect models were constructed to reveal the differences in factors influencing branch occlusion, knot size, and discoloration between natural and artificial pruning treatments. The mixed-effect models indicated that the most important factor in predicting branch occlusion time, dead knot radius, total knot radius and discoloration length was branch diameter for artificial pruning and dead branch stub length for natural pruning. The dead branch stub length was also closely and positively correlated with branch diameter under natural pruning. Branch occlusion time was negatively correlated with stem diameter growth rate during the period of branch occlusion while discoloration length was positively correlated with branch occlusion time for both treatments. In addition, acute branch insertion angle increased the size of dead knot and discoloration. It was concluded that artificial pruning promotes faster branch occlusion, reduces knot sizes and does not lead to stem discolorations, and should hence be applied in the plantation management of this species.