With the increasing depletion of high-quality raw materials, siliceous limestone, sandstone and other hard-to-burn raw materials containing crystalline SiO₂ are gradually being used to produce clinker. This study investigates the influence of the quartz content and particle size in siliceous limestone on the calcination process and the resultant quality of cement clinker. Two different siliceous limestones were grinded to different fineness, and calcinated with some other materials. The content of the clinkers was analyzed with the XRD–Rietveld method and the microstructure of the clinkers was observed with laser scanning confocal microscopy (LSCM) and field emission scanning electron microscopy (FESEM). Three key outcomes of this study provide new insights on the use of siliceous limestone in cement production, namely that (i) reducing the fineness values of siliceous limestone from 15% to 0% of residue on a 0.08 mm sieve decreases the quantity of these larger quartz particles, resulting in an increase in C₃S content by up to 8% and an increase in 28d compressive strength by up to 4.4 Mpa, which is 62.30 Mpa; (ii) the morphology of quartz—either as chert nodules or single crystals—affects the microstructure of C₂S clusters in clinker, finding that chert nodules result in clusters with more intermediate phases, whereas large single crystals lead to denser clusters; (iii) the sufficient fineness values of siliceous limestone SL1 and SL2 are 5% and 7% of residue on a 0.08 mm sieve, respectively, which can produce a clinker with a 28d compressive strength greater than 60 Mpa, indicating that for different kinds of quartz in siliceous limestone, there is an optimum grinding solution that can achieve a balance between clinker quality and energy consumption without having to grind siliceous limestone to very fine grades.