Since 2015, six typical masonry cultural relics around the China’s UNESCO World Heritage Site — the West Lake Cultural Landscape of Hangzhou have been systematically monitored from three aspects: deterioration patterns, physical and mechanical properties, and the changes of the micro-environment, using non-destructive testing equipment like optical microscope, ultrasonic pulse wave, Schmidt hammer, surface roughness tester, thermohygrometers, rain gauges, air quality monitors and so on. High-throughput sequencing technology had also been used to study distribution and diversity of microorganisms on the surface of masonry. Results show that the deterioration of relics can be reflected by their physical and mechanical properties, comprehensive evaluation of the heritage’s health state can be made through long-term continuous monitoring. It also found that different deterioration pattern will occur with different types of materials or in different preservation conditions, marble artifacts which completely exposed outdoors tends to significant degradation in just five years due to temperature fluctuations and acid rain. Besides, Microorganisms’ growth and propagation correlate positively with environmental conditions. As a case study, this paper described in detail the whole process of monitoring the deterioration of masonry relics at a UNESCO World Heritage sites, which may provide some references for researchers in similar fields.