To improve the sensitivity of fluorescence detection, a microfluidic channel structure using silicon-based photonic crystals is proposed. The microfluidic channel can effectively enhance the excitation light field and realize fluorescence-directed emission of quantum dots. The band structure of the photonic crystal was determined by the plane wave expansion method. The effects of quantum dot polarization, channel structure parameters, and the position of quantum dots in the channel on fluorescence emission were examined using the finite-difference time-domain method. In addition, the enhancement effect of the structure during the excitation of quantum dots was analyzed. The simulation results show that, compared with the traditional silicon microfluidic channel, the photonic crystal microfluidic channel has a higher far-field emission power and a narrower radiation angle. Compared with the glass substrate, the far-field power of quantum dots in the microfluidic channel of the photonic crystal achieves a 16.9-fold enhancement and a narrow-angle emission within 9°. The photonic crystal microfluidic channel achieves an average 7.9-fold enhancement of the excitation field at 945 nm.