HVAC&R system costs can often be one of the most expensive components, representing approximately 15% of the total construction cost for office buildings. Despite their significant importance, there is a lack of a consistent and homogeneous framework to approximate the estimate research. This research deals with the prediction methodology of HVAC&R system cost with the aim of establishing a common idea for the analysis of the construction cost estimate. Our approach deals with the concept of an HVAC&R set that is composed of subsystems. The matrix combination analysis is examined, and total 960 HVAC&R system cost estimation can be implemented to large scale office buildings.