Porous carbon materials are used for many electrochemical applications due to their outstanding properties. However, research on controlling the pore structure and analyzing the carbon structures is still necessary to achieve enhanced electrochemical properties. In this study, mesoporous carbon nanotube (CNT)-carbon nanofiber electrodes were developed by heat-treatment of electrospun starch with carbon nanotubes, and then applied as a binder-free electrochemical electrode for a lithium-ion battery. Using the unique lamellar structure of starch, mesoporous CNT-carbon nanofibers were prepared and their pore structures were controlled by manipulating the heat-treatment conditions. The activation process greatly increased the volume of micropores and mesopores of carbon nanofibers by etching carbons with CO2 gas, and the Brunauer-Emmett-Teller (BET) specific area increased to about 982.4 m2·g−1. The activated CNT-carbon nanofibers exhibited a high specific capacity (743 mAh·g−1) and good cycle performance (510 mAh·g−1 after 30 cycles) due to their larger specific surface area. This condition presents many adsorption sites of lithium ions, and higher electrical conductivity, compared with carbon nanofibers without CNT. The research suggests that by controlling the heat-treatment conditions and activation process, the pore structure of the carbon nanofibers made from starch could be tuned to provide the conditions needed for various applications.