An effective fast plasma position control (FPPC) method using in-vessel poloidal field coils and capable of maintaining high-elongation plasma, and hence high vertical instability growth, was developed utilizing an magneto-hydrodynamic equilibrium simulation code ‘MECS.’ First, the vertical instability was investigated. It was found that the plasma boundary moves faster than the plasma center due to vertical instability, indicating that boundary-focused control, here called ISO-FLUX scheme, is more effective by accounting for the plasma non-rigidity than schemes focused on the plasma vertical position. In JT-60SA, the ISO-FLUX scheme, in combination with a frequency separation technique, which serves to reduce high-frequency magnetic flux residuals at the control points around the plasma boundary, is employed in the control by in-vessel poloidal field coils. As a result, MECS simulations predict the stable operation of JT-60SA at a target plasma current of 5.5 MA with high elongation (κ ∼ 1.94), even during poloidal beta collapse. These findings highlight the importance of considering non-rigid plasma displacement in FPPC, offering valuable insights for real-time plasma equilibrium control in future nuclear fusion reactors.