The protection of architectural heritage needs continuous detection and analysis. The dissemination of information modeling of Heritage Building Information Modeling (HBIM) has opened up a new channel for the management and protection of architectural heritage. The Morrison chapel, located in Macao, is the only Christian site in the historical urban area of Macao, a world cultural heritage site. In this paper, two different 3D laser scanners are used to carry out digital surveying and mapping of the Morrison chapel to obtain a complete and accurate 3D model. In addition, thermal imaging, hygrometer, XRF carry out disease analysis and detection on the building, and mark and identify the disease on the three-dimensional model, which is helpful for the analysis and protection of the church. This work demonstrates an effective method for 3D data collection of architectural heritage, as well as the positioning, identification and detection of architectural diseases in the model. This digital method for the detection and positioning of architectural heritage diseases is an effective tool for the maintenance and repair of architectural heritage.