Greenhouse gas emission has been a serious problem for decades. Due to the high energy consumption of traditional construction and building materials, recycled aggregate and other environmentally-friendly materials or recycled materials have been researched and applied. The treatment and reuse of construction and demolition waste (CDW) is a good way to reasonably distribute the renewable resources in the urban city. The recycled aggregate can be used in road engineering, geotechnical engineering and structural engineering. The combined use of natural aggregate and recycled aggregate may possess better performance in real constructions. This paper investigates the mechanical performance, micro-mechanism and CO2 footprint assessment of NAM (natural aggregate mortar) and RAM (recycled aggregate mortar). Compressive strength test, flexural strength test, XRD and SEM, and CO2 emission evaluation were conducted and analyzed. The results indicate that NAM depicts better compressive strength performance and RAM has higher flexural strength. The XRD and SEM patterns illustrate that the ettringite and C-S-H are the most important role in shrinkage-compensating mechanism, which is more obvious in RAM specimens. The proportion of CaO and MgO hydrated into Ca(OH)2 and Mg(OH)2 is also a key point of the volume expansion through the curing period. Finally, the CO2 emission of NA is higher than RA per unit. This indicates that utilizing recycled aggregate over other conventional resources will reduce the energy consumption, and hit the mark to be environmental-friendly.