Catalyst design plays vital roles in structurally relevant reactions. Revealing the catalyst structure and chemistry in the reactive environment at the atomic scale is imperative for the rational design of catalysts as well as the investigation of reaction mechanisms, while in situ characterization at the atomic scale at high temperature is still a great challenge. Here, tracking intermetallic Co7W6 nanocrystals with a defined structure and a high melting point by environmental aberration-corrected transmission electron microscopy in combination with in situ synchrotron X-ray absorption spectroscopy, we directly present the structural and chemical stability of the Co7W6 nanocrystals in methane, carbon monoxide, and hydrogen at temperatures of 700-1100 degrees C. The evidence is in situ and in real time with both atomic scaled resolution and collective information. The results are helpful in revealing the mechanism of structural-specified synthesis of single-walled carbon nanotubes. This research offers an example of systematic investigation at the atomic scale on catalysts under reactive conditions. Such catalysts presenting high structural stability may also find applications in other structure-specific synthesis.