π-Conjugated molecule bridged silicon quantum dots (Si QDs) cluster was prepared by Sonogashira C−C cross-coupling reaction between 4-bromostyryl and octyl co-capped Si QDs (4-Bs/Oct Si QDs) and 1,4-diethynylbenzene. The surface chemical structure, morphology, and chemical composition of the Si QD cluster were confirmed by Fourier transform infrared spectroscopy, field emission transmission electron microscopy, and energy-dispersive X-ray spectroscopy. Lithiumion batteries were fabricated using 4-Bs/Oct Si QD and Si QD clusters as anode materials to investigate the effect of QD clustering on the electrochemical performance. Compared with the 4-Bs/Oct Si QD electrode, the Si QD cluster exhibits improved electrochemical performance, such as a high initial discharge capacity of ∼1957 mAh/g and good cycling stability with ∼63% capacity retention following 100 cycles at a current rate of 200 mA/g when tested at the voltage window of 0.01−2.5 V. The improved electrochemical performance of the Si QD cluster is attributed to the π-conjugated molecules between the Si QDs and on the surface of Si QD cluster, which serve as a buffer layer to alleviate the mechanical stresses arising from the alloying reaction of Si with lithium and maintain the electrical conduits in the anode system.