We describe an ion source based on the spontaneous desorption process. The production, acceleration, and separation processes allow for the production of keV energy polyatomic ions while maintaining a high signal‐to‐background ratio. Both atomic and polyatomic ions with up to 37 keV energy were generated. Because the spontaneous desorption process is naturally pulsed, the ion source was attached to a dual time‐of‐flight mass spectrometer for secondary ion mass spectrometry experiments. In this article, we describe the design of both the polyatomic ion source and the mass spectrometer.