In an effort to comprehensively study the wood property variation in juvenile wood, compression wood, and mature wood, and also to provide a rapid and cost-effective assessment tool to screening the wood chemical property variation, several loblolly pines (Pinus tadea), and transmittance near infrared spectroscopy were utilized in this study. The method development results show that a successful screening of wood chemical property variation, such as lignin and α-cellulose contents, could be adapted using stacked wood wafers microtomed from increment cores and combining with transmittance near infrared spectroscopy. The morphological, chemical, and metabolic analyses of juvenile wood and compression wood show that although compression wood and juvenile wood share some properties, they are actually distinct in their chemistry during development and in final wood chemistry and anatomy. The within tree variation analyses also show that juvenile wood from the top of the tree and that from the base of the tree are more different in morphological structures than in chemical structures. A similar pattern was found between juvenile wood and mature wood. The results obtained suggest that the within tree compression wood percentage and the fiber quality differences inherent in juvenile wood appear to have a greater influence on the final wood products.