The purpose of this study is to compare the differences among neck muscle fatigue evaluation algorithms and to find a more effective algorithm which can provide a human factor quantitative evaluation method for neck muscle fatigue during bending over the desk. We collected surface electromyography signal of sternocleidomastoid muscle of 15 subjects using wireless physiotherapy Bio-Radio when they bent over the desk using memory pillows for 12 minutes. Five algorithms including mean power frequency, spectral moments ratio, discrete wavelet transform, fuzzy approximation entropy and the complexity algorithms were used to calculate the corresponding muscle fatigue index. The least squares method was used to calculate the corresponding coefficient of determination R2 and slope k of the linear regression of the muscle fatigue metric. The coefficient of determination R2 evaluates anti-interference ability of algorithms. The maximum vertical distance Lmax which is obtained by the Kolmogorov-Smirnov test for the slopes k evaluates the ability to distinguish fatigue of algorithms. The results indicate that in the aspect of anti-interference ability, the fuzzy approximation entropy has the largest R2 when using memory pillows with different heights. When the fuzzy approximate entropy is compared with average power frequency or the discrete wavelet transform, the differences are significant (P < 0.05). In terms of distinguishing the degree of fatigue, the approximate entropy is still the largest, with a maximum of 0.496 7. Fuzzy approximation entropy is superior to other algorithms in ability of anti-interference and distinguishing fatigue. Therefore, fuzzy approximation entropy can be used as a better evaluation algorithm in the evaluation of cervical muscle fatigue.