A facile strategy is developed to synthesis selenium/carbon composites (Se@CNFs-CNT) by co-heating Se powder and electrospun Polyacrylonitrile (PAN)-CNT nanofibers at 600°Cin a sealed vessel. The Se molecules are chemically bonded and physical encapsulated by carbonized PAN-CNT composite (CNFs-CNT), which leads to prevent the dissolution of polyselenide intermediates in carbonate based electrolyte. When directly used as flexible free-standing cathode material for Li–Se batteries in low cost carbonate-based electrolyte, the Se@CNFs-CNT electrode exhibits improved cyclability (517 mAh g−1 after 500 cycles at 0.5 A g−1) and rate capability (485 mAh g−1 at 1 A g−1). Moreover, when tested as sodium batteries, it maintains a reversible capacity of 410 mAh g−1 after 240 cycles at 0.5 A g−1. The superior electrochemical performance (especially at high rates) of Se@CNFs-CNT is attributed to synergistic effect of the additive of CNT, the well confine of Se in the CNFs-CNT matrix through chemical bonding and the 3D interconnected carbon nanofibers (CNFs). This simple yet efficient process thus provides a promising route towards fabrication of a variety of high performance flexible Li–Se and Na–Se batteries.