In response to the difficulties posed by traditional microscopy imaging techniques in capturing the structure and thickness of colorless transparent samples, we have designed a miniature three-dimensional reconstruction system for such samples. This innovative system, breaking away from traditional optical structures, performs phase retrieval on transparent samples to achieve three-dimensional reconstruction. It requires only light carrying sample information, which is then bifurcated by a spectroscope and captured by a stereo camera. Constructed using 3D printing technology, the compact system measures just 110 mm×110 mm×60 mm, offering a cost-effective solution that is also compatible with traditional microscopy imaging equipment. It incorporates autofocus and field of view correction algorithms, which, by collecting one over-focused and one under-focused image, solve the transport intensity equation to enable phase retrieval and hence the three-dimensional reconstruction of transparent samples. Test results have shown that the system can achieve an imaging resolution of 2.46 μm under a 10× objective lens, and the phase recovery accuracy can also meet the basic requirements. Furthermore, the successful three-dimensional reconstruction of blood cells and scratches on microscope slides validates the system's feasibility and practicality.