Zn-organic batteries (ZOBs) are promising energy-storage device owing to their merits of high capacity, low cost, and sustainability. However, their electrochemical performance is limited by irreversible organic small-molecular cathode due to the shuttle effect of discharge intermediates. Here, we report on the use of a chemically cross-linked poly(vinyl alcohol) films with halloysite nanotubes (GA-PVA/HNTs) as a separator for ZOBs. The GA-PVA/HNTs separator with intrinsic electro-negativity of HNTs act as permselective shield for negatively redox organic resultants, thereby preventing the shuttling effect without sacrificing power. In order to illustrate the superior performance of the GA-PVA/HNTs separator, a battery using as-prepared GA-PVA/HNTs separator, benzoquinone (BQ) as the cathode and Zn as the anode displays a high initial capacity (435 mAh g−1 at 0.3C) and superior cycle performance (98% capacity retention after 200 cycles at 3C). Moreover, a flexible Zn||BQ battery based on GA-PVA/HNTs separator is constructed, achieving a highly stable capacity of 431 mAh g−1 under different bending conditions. This work promotes the development of high absorptivity separator for the flexible zinc batteries.