This article reports on the limitation analyses for the sidewall angle (SWA) measurements of microstructures with a confocal laser scanning microscope (CLSM). Under the resolutions of three-dimensional imaging process of CLSM and its spatial frequency spectrum distribution, the optical phase signal of an object is studied to model the signal-noise-ratio (SNR) performance of measurements and the point spread function theory is applied to discuss the limitation to the measurement accuracy of SWA. Then, the characteristics of both the relative SNR performance and the measurement accuracy are numerically simulated with these two theoretical models. As a result, two important characteristics of CLSM measurements for SWA are found as that the relative SNR is quickly decreasing with SWA; the intrinsic measurement error linearly decreases with SWA. Furthermore, for a fabricated device sample having the waveguide dimension of 6 × 10 µm2, with a scanning section of 10nm and a detector aperture of PH = 0.3 Airy Unit, a CLSM image of 300 × 300 µm2 is acquired and reconstructed, in which 10 waveguide channels is covered. For a selected channel, based on ten measurements the averaged values of the left and right SWAs are 85.68° ± 0.32° and 86.59° ± 0.24°, respectively, after being compensated with the intrinsic measurement errors. Finally, the distribution and uniformity of SWA values among the ten waveguide channels in the image are analyzed.