In the soils of western Jilin Province in northeastern China, some significant gaps have been observed between the fraction of the soil existing as clay-size particles (<0.002 mm) and the amount attributable to crystalline clay minerals, and that the relative proportions of crystalline clay minerals to the total clay-size fraction (CP) apparently varies with latitude. The purpose of the present study was to identify the reason for this discrepancy and to explain the dependence on latitude. The grain sizes and mineral compositions of the whole soils from western Jilin Province, China, were analyzed by laser particle-size analysis (LPSA) and X-ray diffraction (XRD), and the <0.002 mm particle-size fraction was analyzed by XRD and X-ray fluorescence (XRF). The results confirmed that the percentage gaps between the clay fraction and clay minerals increased with increasing latitude. The theoretical illite percentage calculated from K2O content was compared with the illite percentage measured by XRD, and the results suggested that the measured illite accounted for only a small proportion of the theoretical illite. Structures of some special minerals below the identification threshold of XRD was suggested to be the reason for the percent gaps. The grain size and mineral crystallization both changed with latitude: the soil particle size and the CP decreased. In addition, clay minerals were more sensitive to climate than particle sizes were, and the CP of clay minerals in the soils within 0~180 cm depth all decreased with increasing latitude; however, the grain size showed patterns with latitude only in relatively shallow soil layers. The present study provides a reference and error analysis for the testing of clay minerals in alpine regions, and more suitable methods may be considered for development of clay-mineral testing in future studies.