The present disclosure provides an exercise guiding system including a sensing module, a calculating module, a converting module and an output module. The sensing module keeps recording an R-R interval of a user doing exercise. The computing module receives the R-R interval from the sensing module and performs heart rate variability analysis on the R-R interval to generate a first output. The converting module receives the first output from the calculating module, recognizes a threshold output of the first output according to a threshold and acquires an anaerobic threshold corresponding to the user according to the threshold output, wherein the anaerobic threshold corresponding to the user is a first heart rate corresponding to the threshold output in the R-R interval. The output module receives the anaerobic threshold from the converting module and outputs an exercise guidance of the user according to the anaerobic threshold.