Agroforestry systems (AFS) are priority semi-natural ecosystems in fragile ecological zones. The complexity and diversity of their species structure play a crucial role in maintaining AFS stability. To explore the optimization of improvement strategies in AFS’ structure and stability for control of karst desertification (KD), in this study, we chose typical desertification control areas in the southern China karst region. The study included homegarden (HG), agrisilviculture (ASV), and multipurpose woodlots (MWLs) as three AFS. We quantified the AFS’ structural characteristics using descriptive statistics and spatial structure parameters. We used the fuzzy integrated evaluation method with structural and functional indicators as guidelines, and stand structure, plant species diversity, soil fertility, and environmental factors as first-level evaluation indicators. The entropy weight method calculates the weights of indicators at all levels. The fuzzy comprehensive evaluation method establishes an evaluation index system to evaluate the grading of AFS’ stability. The results showed that: (i) The species composition of the AFS in the KD control areas had a simple structure, the overall diversity level was low, and the diversity level of herbaceous plants was better than that of woody plants. (ii) The overall distribution curves of diameter at breast height (DBH), tree height (TH), and crown width (CW) of woody plants in the AFS in the KD control areas were slight to the left, with a single-peaked pattern, mostly randomly and unevenly distributed in space, with a low degree of tree species isolation and relatively weak stand stability. (iii) There was variability in the stability classes of different types of AFS, overall reflecting the ranking HG > ASV > MWLs. (iv) When structural optimization was applied, corresponding measures can be taken according to farmers’ wishes for different types of AFS and their primary business purposes. The improvement of stability depends mainly on the utility of the structural optimization applied coupled with positive human interference (for example, pruning, dwarfing, and dense planting). This study provides a scientific reference for maintaining the stability of AFS and promoting service provision.