Ten CMS lines and three R lines were crossed using a line × tester mating design to assess the combining ability for yield and component characters in sunflower (Helianthus annuus L.). Fourier Transform Infrared Spectroscopy (FTIR), fatty acid profiling and protein content analysis of thirty developed hybrids and their parents were conducted to identify and estimate the relative amounts of various bioactive compounds in sunflower. The analysis of variance showed significant variation among lines as well as testers for all the traits under study indicating presence of substantial genetic variation. The line CMS-519 was observed as good general combiner for plant height, head diameter, stem diameter, number of leaves/plants, seed yield/plant, biological yield/plant, where as CMS-240 was good general combiner for oil content and volume weight. Among the testers GP4-1424 was identified as a good general combiner for most traits. Among the hybrids, CMS-519 × GP4-1424 exhibited the highest specific combining ability (SCA) for plant height, head diameter, stem diameter, biological yield per plant and seed filling percentage. The cross CMS-207 × RHA-1-1 and CMS-243 × GP4-1424 showed highest SCA for seed yield and oil content respectively. Fatty acid composition analysis revealed that the hybrids were rich in unsaturated fatty acids, particularly oleic and linoleic acids. FTIR analysis confirmed the presence of functional groups such as =C-H, -C-H (CH3), -C-H (CH2), -C=O (ester), -C-O, -(CH2) n-. Crosses such as CMS-240 × IR-6, CMS-243 × GP4-1424, HA-89 × IR-6 and CMS-519 × GP4-1424 were superior in terms of both oil yield and protein content.