This study investigated the impact of cement clinker percentages on the alkali-silica reaction (ASR) mechanisms of aggregates with varying alkali-silica reactivity. Experimental findings indicated that the low-heat Portland cement (LHC) mitigated the development of the ASR process in soda-lime glass aggregate (SLGA) concrete. The ASR in ordinary Portland cement (OPC) mainly initiated within the SLGA, leading to crack propagation through the matrix. The in-situ X-ray micro-computed tomography test indicated that LHC altered the manifestation of ASR in concrete containing SLGA, leading to different destructive forms. Specifically, ASR between the LHC and SLGA primarily occurred at the periphery of the SLGA. The in-situ quantity analysis results illustrated that the LHC mitigated the ASR-induced cracks in the SLGA concrete. For the less alkali-reactive natural aggregate, the effect of LHC cement on ASR was diminished. ASR still only occurred within the natural aggregate concrete, distributing in highly alkali-reactive phases inside the aggregates. The chemical analysis results supposed that the differing ASR pathways could be attributed to the interaction between the calcium content in the LHC and the spatial distribution of alkali-reactive phases within the aggregates. These findings help interpret the mechanism of the slower ASR process in the belite-rich cement concrete.