To assess the influence of bridge structure manipulation on the electrochemical performance of π-conjugated molecule-bridged silicon quantum dot (Si QD) nanocomposite (SQNC) anode materials, we prepared two types of SQNCs by Sonogashira cross-coupling and hydrosilylation reactions; one is SQNC-VPEPV, wherein the Si QDs are covalently bonded by vinylene (V)–phenylene (P)–ethynylene (E)–phenylene–vinylene, and the other is SQNC-VPV. By comparing the electrochemical performances of the SQNCs, including that of the previously reported SQNC-VPEPEPV, we found that the SQNC with the highest specific capacity varied depending on the applied current density; SQNC-VPEPV (1420 mA h g⁻¹) > SQNC-VPV (779 mA h g⁻¹) > SQNC-VPEPEPV(465 mA h g⁻¹) at 800 mA g⁻¹, and SQNC-VPV (529 mA h g⁻¹) > SQNC-VPEPEPV (53 mA h g⁻¹) > SQNC-VPEPV (7 mA h g⁻¹) at 2000 mA g⁻¹. To understand this result, we performed EIS and GITT measurements of the SQNCs. In the course of investigating the lithium-ion diffusion coefficient, charge/discharge kinetics, and electrochemical performance of the SQNC anode materials, we found that electronic conductivity is a key parameter for determining the electrochemical performance of the SQNC. Two probable causes for the unique behavior of the electrochemical performances of the SQNCs are anticipated: (i) the SQNC with predominant electronic conductivity is varied depending on the current density applied during the cell operation, and (ii) the degree of surface oxidation of the Si QDs in the SQNCs varies depending on the structures of the surface organic molecules of the Si QDs and the bridging molecules of the SQNCs. Therefore, differences in the amount of oxides (SiO₂)/suboxides (SiO_x) on the surface of Si QDs lead to significant differences in conductivity and electrochemical performance between the SQNCs.