Operation regulations of two main electron transport pathways in nectarine (Prunus persica var. nectariana cv. Shuguang) buds during endodormancy induction were studied to understand possible roles which two main electron transport pathways played in the buds of deciduous fruit trees during endodormancy induction. Respiratory inhibitors (KCN and SHAM) were used to investigate total respiration rate (Vt), the development and operation of the alternative pathway and partitioning of electrons between the cytochrome and alternative pathways in nectarine buds during endodormancy induction. Results indicated that changes of Vt in flower and leaf buds showed single and double hump-shaped curves, respectively. In endodormancy induction, the capacity (Valt) and activity (ρValt) of the alternative pathway rapidly increased, but changes of them had different patterns during the entire measuration. At the same time, changes of engagements of the alternative (ρValt/Vt) and cytochrome pathway (ρ′Vcyt/Vt) were opposite, and ρ′Vcyt/Vt was always further higher than ρValt/Vt during the entire measuration. All these results indicated that the development and operation of the alternative pathway played important roles in endodormancy induction, but the cytochrome pathway was the main pathway for mitochondrial electron transport in buds during endodormancy induction. Operation regulations of two main electron transport pathways in nectarine (Prunus persica var. Nectariana cv. Shuguang) buds during endodormancy induction were learned to understand possible roles which two main electron transport pathways played in the buds of deciduous fruit trees during endodormancy induction. (KCN and SHAM) were used to investigate total respiration rate (Vt), the development and operation of the alternative pathway and partitioning of electrons between the cytochrome and alternative pathways in nectarine buds during endodormancy induction. Results indicate that changes of Vt in flower and leaf buds showed single and double hump-shaped curves, respectively. In endodormancy induction, the capacity (Valt) and activity (ρValt) of the alternative pathway rapidly increased, but changes of them had different patterns during the entire measuration. At the same time , changes of engagements of the alternative (ρValt / Vt) and cytochrome pathway (ρ Vcyt / Vt was always more higher than ρValt / Vt was always more than ρValt / Vt during the entire measuration. All these results indicates that the development and operation of the alternative pathway plays important roles in endodormancy induction, but the cytochrome pathway was the main pathway for mitochondrial electron transport in buds during endodormancy induction.