Metal phthalocyanine with a unique π-conjugated structure, has shown extraordinary promise for electrocatalysis, batteries and supercapacitors. High-performance Zn-ion hybrid supercapacitors make high demands on the energy storage mechanisms of metal phthalocyanine. We propose a β-form zinc phthalocyanine (ZnPc) molecular crystal as a cathode material for flexible Zn-ion hybrid supercapacitors. The β-ZnPc is facilely synthesized through the annealing treatment of the original ZnPc, which is previously fabricated through a ring-closure reaction assisted by catalysis of sodium methanol and ultrasonic treatment. The structural transformation of ZnPc from α-ZnPc to β-ZnPc is demonstrated at the annealing temperature from 200 °C to 300 °C, probably attributed to the short-range neighbor interaction between the adjacent ZnPc molecular layers. The β-ZnPc electrode exhibits the higher specific capacitance and the better rate capability than those of the α-ZnPc electrode, mainly due to its higher specific surface area and more abundant pore structure. The electron density and adsorption energy of ZnPc are theoretically calculated, revealing the active N sites for the reversible adsorption/desorption of Zn2+. The flexible Zn-ion hybrid supercapacitor provides the maximum energy density of 86.2 Wh kg−1 at 0.22 kW kg−1, and maintains the capacitance retention of 73.4% after 100,000 cycles, opening up a new avenue for developing high-energy and long-life Zn-ion hybrid supercapacitors.