Detecting the z-position of moving objects in an embedded microchannel is an important but highly challenging problem in the MEMS field. The present study proposes a new depth measurement system based on the chromatic aberration effect under a dark-field illumination scheme. The microchannel is illuminated by dispersed white light and the light scattered from the moving objects is captured by a low numerical aperture (N.A.) objective lens. Due to chromatic aberration effect, sample in various positions will scatter different wavelengths. The depth of each moving object is then determined by inspecting the intensity ratio of the scattered spectral components with wavelengths of 450 nm (blue light) and 670 nm (red light), respectively. Experimental results show that the proposed system enables the object depth to be measured over a range of ±15 μm while using acrylic lens for light aberration. Alternatively, the developed system is capable to discriminate the depth change of 2 μm micro-beads when a higher Abbe number material of BK7 lens is used for light aberration. The depth measurements are obtained without the need for a delicate optical system or scanning process with the developed system. The use of UV-Vis-NIR spectrometer enables this system to analyze the depths of the samples in flow velocity 500 μm/sec. The proposed system provides a straightforward yet highly effective means of determining the depth of moving objects in microfluidic channels in a continuous manner.