A system and a method of guiding a real-time inspection using a 3D scanner are provided. The system and the method of guiding a real-time inspection using a 3D scanner allow an operator to perform an accurate and swift inspection of an object to be measured so as to meet a designer's design intentions. For that purpose, 3D shape information of an object to be measured is detected using a scanner and shape information and inspection guide information of the object stored in a data storage unit, and inspection information of the object for judging the validity of the measurement information detected from the scanner is checked through a display unit. After that, the scanner is operated to compare the measurement information detected by the scanner with the inspection information so as to judge the validity of the measurement. Therefore, an operator can accurately understand a designer's intentions for inspection to perform measurement.