Applying a radian phase shift other than 2π is a key issue for superconducting circuits, such as flux qubits. The magnetic flux is useful when generating a phase shift. However, a quantized magnetic flux accompanying a trapped vortex in a superconductor does not have a phase shifter function. The magnetic flux generated by an external field generates noise. In this study, we propose a phase bias system that does not require an external field during operation. We confirm the phase shift of a direct current superconducting interference device (SQUID) placed on an ultrathin superconducting Nb bilayer with a through-hole by cooling it to a temperature below the superconducting transition temperature with an external field. Although the cause of the phase shift in our system is unclear, we believe that it may be caused by a fractional quantum in the bilayer. When the SQUID is replaced by a qubit, the phase shift can be applied to a phase bias.