Bridging optical tweezers and microfluidics can form a multifunctional platform, which can overcome the difficulties of precise manipulation in hydrodynamic flow in a noninvasive method. However, when integrated into a microfluidic chip, the fiber optic tweezer loses its flexibility. Here, we propose a compact single fiber optical tweezer–micropipette system. It can sort particles by differences in shape and refractive index in a completely noninvasive way while retaining the flexibility, high selectivity, and precision of a fiber optical tweezer. Compact microfluidic channels are formed by combining two different-diameter micropipettes. The internal diameter of the circular microfluidic channel is less than 30 μm. Furthermore, we calculated the trapping and pushing regions of Yeast and Chlorella and achieved the separation of Yeast from Chlorella in the experiments. We did 90 sets of tests on the sorting accuracy of single fiber optical tweezer (SFOT). SFOT was able to distinguish between two types of particles in each test. With the advantages of high selectivity, high accuracy, low optical power consumption, and compact structure, such methods can be used in the fields of optical separation, cell transportation, cell sorting, and single-cell analysis.