The morphology and causes of stacking faults (SF) in homoepitaxial layers of 4H-SiC were studied. According to characteristics of PL images and morphology images of 4H-SiC five kinds of SFs have been defined. In the PL images, the morphologies of SF I and SF II-V are trapezoidal and triangular, respectively. SF II lays inside the area of SF I. In the morphology images, SF I and IV are not seen, SF II-III are carrot shaped and SF V is triangular respectively. The results show that SF I is a kind of base plane SF which originates from the base plane dislocation (BPD) lines of the substrate, parallel to <1$\bar{1}$00> direction and moving along <11$\bar{2}$0> direction during epitaxial growing. SF II and most of SF III-IV originate from BPDs in substrate. One BPD converts into threading dislocation during epitaxial growing and propagates to the surface along <0001> direction, while other BPDs or partial dislocations originating from threading dislocation propagate in (0001) plane to form triangular base plane SFs. The rest of SF III-IV and SF V originate from TED or other defects in substrate. SF II-III display carrots morphology because a prism SF plane perpendicular to the (0001) plane is formed to intersect with surface during epitaxial growing process. SF IV is not seen in the morphology image because no prism SF plane is formed to intersect with surface. All results demonstrated that reducing BPDs of the substrate is especially important for reducing SFs in the epitaxial layers.