Pecans [Carya illinoinensis (Wangenh.) K. Koch] are one of the most valuable tree nuts native to North America. Their kernels are a source of important nutrients and bioactive compounds. Depending on the cultivars, the two-year average for TPC, FRAP and H-ORACFL values ranged from 0.72 to 1.59 g ellagic acid equivalents/100-g nutmeat, 7.76 to 18.77 mmol Fe2+ equivalents/100-g nutmeat, and 8.87 to 21.24 mmol Trolox equivalents/100-g nutmeat, respectively. Although the total phenolics content and antioxidant capacities differed significantly across cultivars, the percentages of crude phenolics on fresh nut bases were yielded little fluctuations. Therefore, a compositional difference is expected. To improve the identification and quantification of pecan phenolics, two fused-core columns were compared for their separation efficiencies on pecan phenolic compounds using a kinetic approach. Results indicated that both types of columns demonstrated comparable performance at separating phenolic acids and flavonoids. But the pentafluorophenyl (PFP) column gave higher plate numbers and superior peak shapes as well as overall separations when analyzing ellagic acid, its derivatives and other dilactones. Using the optimized chromatographic method, a standard set of phenolic compounds were revealed in pecan phenolic fraction. HPLC-QTOF-ESI-MSn suggested that ellagic acid, its derivatives, and proanthocyanidins (PACs), mostly of two and three degrees of polymerization, to be the prominent contributors. It is indicated that variations in antioxidant capacities resulted from the differences in concentrations of the endogenous phenolic compounds rather than the types present. In addition, antioxidant capacities of pecan can be greatly boosted by pruning practice, even at a triannual frequency. This unique approach was able to utilize the current findings in the field of pecan physiology to improve productivity and nut quality. The outcomes are expected to provide growers with cost-effective options to increase the pecan nut production and quality. Aroma-active compounds were separated and identified using HS-SPME-MS for the first time A total of 72 flavor-active compounds were identified and quantified in roasted samples, of which 16 were unique to the roasted pecans relative to their raw counterparts.