This weak signal detection system has: a statistical data acquisition unit which measures the average value or distribution of an input signal in which is noise superimposed on a desired signal, calculates parameters such as the amplitude or noise dispersion of the desired signal, and outputs the calculated data obtained thereby; a nonlinear characteristic unit which outputs a signal having a nonlinear response with respect to the magnitude of the voltage or the current of the input signal; a signal detection ratio evaluation unit which determines whether the output signal from the nonlinear characteristic unit is the desired signal, calculates the detection ratio in the event that the signal is the desired signal, and outputs detection ratio data; a parameter adjustment unit which, on the basis of detection ratio data obtained by the signal detection ratio evaluation unit and calculated data obtained by the statistical data acquisition unit, adjusts a control parameter pertaining to the responsiveness of the nonlinear characteristic unit; and a signal processing unit which performs signal processing of the output signal of the nonlinear characteristic unit, and conversion to digital data or image data. In so doing, it is possible to provide a weak signal detection system having improved signal detection accuracy, and an electron microscope equipped with the system.