This study aimed to identify insertion–deletion (InDel) variants in key genes of the Hippo signaling pathway in four Chinese sheep breeds: Tong sheep (TS), Hu sheep (HS), Small Tail Han sheep (STHS), and Lanzhou large-tailed sheep (LLTS). InDel variants in MST1/2, LATS1/2, SAV1, MOB1A/B, and YAP/TAZ genes were screened using public databases and identified through PCR amplification, gel electrophoresis, and sequencing. This study identified significant associations between InDel variants and growth traits across the four breeds. Specifically, three loci in the MST1 gene were significantly associated with chest circumference, body height, and body weight in STHS, HS, and TS. Four loci in MST2 influenced hip height, body weight, and chest circumference across all breeds (p < 0.05). Additionally, two loci in YAP significantly affected body height, chest circumference, and body length in LLTS, STHS, and TS, while three loci in the MOB1A gene strongly impacted cannon circumference in all breeds (p < 0.05). These InDel variants may serve as potential molecular markers for breeding. These findings highlight the potential of these InDel variants as molecular markers for sheep breeding and provide valuable resources for improving growth traits in sheep through molecular breeding.