The noise characteristics of a stacked CMOS active pixel sensor (SCAPS) for incident charged particles have been analyzed under 4.5keV Si⁺ ion irradiation. The source of SCAPS dark current was found to change from thermal to electron leakage with decreasing device temperature. Leakage current at charge integration part in a pixel has been reduced to 0.1electronss⁻¹ at 77K. The incident ion signals are computed by subtracting reset frame values from each frame using a non-destructive readout operation. With increase of irradiated ions, the dominant noise source changed from read noise, and shot noise from the incident ions, to signal frame fixed-pattern noise from variations in sensitivity between pixels. Pixel read noise is equivalent to ten incident ions. The charge of an incident ion is converted to 1.5electrons in the pixel capacitor. Shot noise corresponds to the statistical fluctuation of incident ions. Signal frame fixed-pattern noise is 0.7% of the signal. By comparing full well conditions to noise floor, a dynamic range of 80dB is achieved. SCPAS is useful as a two-dimensional detector for microanalyses such as stigmatic secondary ion mass spectrometry.