Cas13 are the only CRISPR/Cas systems found so far, which target RNA strand while preserving chromosomal integrity. Cas13b or Cas13d cleaves RNA by the crRNA guidance. However, the effect of the characteristics of the spacer sequences, such as the length and sequence preference, on the activity of Cas13b and Cas13d remains unclear. Our study shows that neither Cas13b nor Cas13d has a particular preference for the sequence composition of gRNA, including the sequence of crRNA and its flanking sites on target RNA. However, the crRNA, complementary to the middle part of the target RNA, seems to show higher cleavage efficiency for both Cas13b and Cas13d. As for the length of crRNAs, the most appropriate crRNA length for Cas13b is 22–25 nt and crRNA as short as 15 nt is still functional. Whereas, Cas13d requires longer crRNA, and 22–30 nt crRNA can achieve good effect. Both Cas13b and Cas13d show the ability to process precursor crRNAs. Our study suggests that Cas13b may have a stronger precursor processing ability than Cas13d. There are few in vivo studies on the application of Cas13b or Cas13d in mammals. With the methods of transgenic mice and hydrodynamic injection via tail vein, our study showed that both of them had high knock‐down efficiency against target RNA in vivo. These results indicate that Cas13b and Cas13d have great potential for in vivo RNA operation and disease treatment without damaging genomic DNA. Graphical and Lay Summary The design of gRNA is crucial for the selection of CRISPR/Cas13 system. Our study shows that 22‐25 nt sgRNA with Cas13b and 22‐30 nt sgRNA with Cas13d can play a good knock‐down role by targeting the middle region of gene transcript. It is easy to downregulate genes in mice by expressing Cas13 in different ways, this allows Cas13b and Cas13d to show great potential for RNA manipulation and disease treatment in vivo without damaging genomic DNA.