Due to harsh environmental limitations, afforestation is particularly difficult in Penghu Archipelago. To improve afforestation success, multi-layer forests have been planted since 1992. In order to assess the stand conditions of the multi-layer forests, this study set up 19 plots on major islands of the Penghu Archipelago to collect data on tree growth, forest soils, and undergrowth plants. The results showed that after the multi-layer forests been planted, Hibiscus tiliaceus and Araucaria excelsa have grown fairly well, and have replaced Casuarina equisetifolia as the dominant species on the stands. Regression analysis showed that wetter soils, loamy soils, and low-alkaline soils were more favorable to stand growth, though the relations were not statistically significant. Survey of undergrowth plants showed that species richness increased as stand age increased. Flowering, fruiting, and regeneration have also been observed for many tree species, suggesting the multi-layer forests will be able to sustain naturally in the future.