Abstract We discuss a supersymmetric extension of a non-relativistic Chern–Simons matter theory, known as the supersymmetric Jackiw–Pi model, in a harmonic trap. We show that the non-relativistic version of the superconformal symmetry, called the super-Schrödinger symmetry, is not spoiled by an external field including the harmonic potential. It survives as a modified symmetry whose generators have explicit time dependences determined by the strength of the trap, the rotation velocity of the system, and the fermion number chemical potential. We construct 1/3 Bogomol'nyi–Prasad–Sommerfield (BPS) states of trapped Jackiw–Pi vortices preserving part of the modified superconformal symmetry and discuss fluctuations around static BPS configurations. In addition to the bosonic massive Nambu–Goldstone modes, we find that there exist massive Nambu–Goldstone fermions associated with broken generators of the modified super-Schrödinger symmetry. Furthermore, we find that eigenmodes form supermultiplets of a modified supersymmetry preserved by the static BPS backgrounds. As a consequence of the modified supersymmetry, infinite towers of explicit spectra can be found for eigenmodes corresponding to bosonic and fermionic lowest Landau levels.