Two-dimensional particle morphology indices face challenges in accurately depicting the characteristics of three-dimensional (3D) manufactured sand (MS), which does not effectively guide the selection of MS for high-performance concrete (HPC). This study aimed to obtain a quantified comprehensive evaluation of actual MS particle groups with specific gradations by thoroughly analysing 3D geometric characteristics. Two representative MS samples were selected for exploration, and river sand (RS) was used as the control. A random selection of sand particles was screened on six sieve levels ranging from 0.15 mm to 4.75 mm. Using X-ray computed tomography and associated image processing technologies, 3D models of these particles were generated, and MATLAB was used to extract their 3D morphology information. Subsequently, the change rules and validity of current 3D particle morphology indicators were examined, focusing on shape, angularity, and texture. Moreover, a comprehensive morphology index, Cm, was proposed by considering the effects of gradation and particle shape classification. The results showed that shape indices more accurately reflected particle characteristics, notably, a higher proportion of spheroid particles, a lower aspect ratio, and greater sphericity correlated with improved particle shape; contrary to traditional beliefs, the angularity index suggested that greater roundness did not necessarily equate to more rounded particles owing to the influence of the proportion of spheroid and cubic particles; meanwhile, texture indices showed minimal difference in the mean values of the 3D fractal dimension for the three types of sand. The proposed index Cm effectively differentiated the particle morphology states of the three sands, with higher Cm values indicating superior particle morphology. The smaller the difference between the Cm values of MS and RS, the better substitute of MS for RS.