Qinghai spruce (Picea crassifolia Kom.) secondary forests in the Qilian Mountains are pivotal for water conservation and biodiversity maintenance in arid northwest China. Based on a 10.2 ha permanent monitoring plot, we employed piecewise structural equation modeling (piecewise SEM) to analyze 47 indicators covering topography, stand structure, ground cover, and soil properties. Canopy openness (CO), moss–litter thickness (MLT), and herbaceous biomass (HB) exerted significant positive effects on the regeneration density (RD) in Qinghai spruce secondary forests, while crown width (CW) exerted a negative regulatory effect on this indicator. HB, altitude (AL), and leaf area index (LAI) exerted positive promoting effects on the regeneration morphometric diversity, whereas soil organic carbon (SOC) imposed strong inhibitory effects on this diversity metric. MLT, AL, SOC, and CW were identified as four shared regulatory factors that simultaneously shape regeneration density and seedling morphometric diversity in these alpine forest ecosystems, verifying the third research hypothesis. Maintaining CO at 0.5–0.6 and retaining 5–6 cm MLT can effectively facilitate natural regeneration. This study provides quantitative threshold references for ecological restoration and refined sustainable management of alpine coniferous spruce forests in arid mountainous regions.