A disease diagnosing method and a disease diagnosing system are provided in the disclosure. The disease diagnosing method includes: obtaining continuous images of a body skin and generating a time domain signal according to an average pixel value of a region of interest in each frame of the continuous images; transforming the time domain signal to a frequency domain signal and combining the time domain signal and the frequency domain signal to a time frequency signal; retrieving multiple first features of a first high dimensional space of the time frequency signal to obtain multiple second features of a second high dimensional space; and use the second features as feature vectors to map to a high dimension feature space, and classifying the second features as one of the multiple categories of a disease corresponding to the region of interest in the body skin according to a hyperplane of the high dimension feature space.