The utility model discloses an orthogonal ion source apparatus. The orthogonal ion source apparatus includes a three-dimensional ionization chamber and an ion lens unit arranged outside the three-dimensional ionization chamber. The three-dimensional ionization chamber includes an ion repulsion electrode, a thermionic emission filament, an electron reception trap, a direct sample introduction pipe, and a sample heating tungsten filament. The ion lens unit includes an ion lead-out lead, an ion focusing electrode, an ion acceleration electrode, and an ion outlet. In the X-axis direction of the ionization chamber, the ion repulsion electrode, the sample heating tungsten filament and the ion lens unit are on the same straight line. In the Y-axis direction of the ionization chamber, the thermionic emission filament and the electron reception trap just face each other. In the Z-axis direction of the ionization chamber, the sample introduction pipe and the heating tungsten filament just face each other. Direct sample introduction of a liquid sample can be achieved, the heating tungsten filament heats an adsorbed sample while carrying out electron bombardment, and background interference is reduced by controlling currents of the heating tungsten filament.