Objective To explore limb coordination patterns and energy flow strategies during the sit-to-stand (STS) transition in individuals with patellofemoral pain (PFP), so as to provide a theoretical evidence for the pathogenesis of PFP and subsequent formulation of treatment and rehabilitation strategies for PFP patients. Methods A totoal of 36 participants was recruited for the STS test. They were divided into the unilateral PFP group (unilateral group), bilateral PFP group (bilateral group), and control group, based on the number of limbs affected by PFP. An infrared motion capture system and a three-dimensioanl force plate were used for motion capture. Visual 3D and Matlab software were used to calculate the trunk and pelvis angles, angular velocities, linear velocities, and proximal and distal joint forces. Additionally, the angles, torques, and joint forces of the hip, knee, and ankle joints, along with the angular and linear velocities of the thigh and shank, were computed. Coupling angles was used to represent coordination patterns via vector coding; the segmental net energy integration method was used to calculate energy flow within segments at each stage. Results For the coordination pattern at frontal plane, the proximal coordination mode frequency of the pelvis-hip coordination in the flexion momentum phase (FMP) was higher in unilateral group than that in bilateral group (P=0.024). In the momentum transfer phase (MTP), the frequency of in-phase coordination in the trunk-pelvis coordination was higher in unilateral group than that in bilateral group (P=0.023), while the frequency of distal coordination was higher in control group than in that in unilateral group (P=0.032). For the knee-ankle coordination pattern, the frequency of distal coordination in control group was lower than that in unilateral and bilateral groups (P=0.025, P=0.005). In segmental energy flow, during the FMP, the energy output from the pelvis during extension phase (MP) was higher in bilateral group than that in control group (P=0.021). Conclusions PFP affects energy flow patterns and coordination patterns at frontal plane during the STS transition. Individuals in unilateral group may engage in lateral pelvic and ankle movements as a dynamic compensation for patellofemoral joint pressure, whereas individuals in bilateral group appear to increase pelvic region energy output and employ a more complex whole-body coordination pattern to compensate for functional deficits in the knee caused by PFP.