The double-focusing mass spectrometer equipped with a superconducting-tunnel-junction (STJ) detector has been applied to measure relative ionization cross-sections for production of ions that are accompanied by different ionic species with the same mass-to-charge ratio (m/z). The STJ detector fabricated for this study enables kinetic energy (E) measurement of incoming individual ions at an energy resolution (ΔE/E) of 15 % with the assistance of an infrared-blocking filter which prevents detector-performance degradation due to infrared radiation illuminating the detector surface at 0.3 K. The high energy resolution is necessary to independently determine both m and z values. One of the limits of conventional mass spectrometry is that it measures the m/z values and thus different ions with the same m/z cannot be analyzed. The unconventional discrimination capability allows direct determination of relative ionization cross-section of the homonuclear diatomic ions ¹⁴N₂²⁺/¹⁴N₂⁺ and ¹⁶O₂²⁺/¹⁶O₂⁺, which are difficult to measure due to the strong interference by the signals of their dissociated atomic ions ¹⁴N⁺ and ¹⁶O⁺ with noticeably large ionization cross-sections. A kinetic-energy-sensitive mass spectrometer is useful for a wide range of analytical chemistry such as ionization processes of multiply ionized molecules and fragmentation of immunoglobulins.