A two seasoned 2020/2021-2021/2022 field experiment was performed in north Sinai governorate, Baloza experimental station, Egypt. Two sunflower varieties (Giza 102 and Sakha 53) were subjected to salinity stress and nano-chitosan encapsulated ascorbic acid (25.7 nm in size) treatments and modified ones with glutathione (48.8 nm in size) and 25 and 50 mg/L chitosan nanoparticles; CH NPs (CH25 and CH50) either individually or loaded with 1 mM glutathione (CH25@Glu and CH50@Glu), compared with the control. The DLS, SEM and FTIR were assigned for the prepared CH NPs. The significant highest increments in biological yield/feddan were obtained by CH50@Glu by Sakha 53 with the highest content of Ѡ-3 fatty acid linolenic and low oleic acid, followed by CH25@Glu for the same variety. Contrarily, the highest biochemical parameters, such as antioxidant activity, were found in Giza 102 at CH25@Glu, followed by CH50@Glu, and the last dose of the same variety had the highest glutathione content.  Sakha 53 variety treated with CH25 generated lesser harmful product, malondialdehyde. In the molecular level, there are no noticeable polymorphic changes in the plant genomic material with polymorphism average of 57.16% for Giza 102 and 46.16% for Sakha 53. So that, Sakha 53 is more stable than Giza102, it also has higher chlorophyll a content than Giza 102. The goal of this study was to compare the secondary metabolites, oil fatty acid composition, genetic uniformity, and productivity of two sunflower varieties under salinity stress and nano-CH treatments. Nano-CH encapsulated with ascorbic acid and loaded with glutathione can be used to maximize the utilization of Sakha 53 sunflower crop and this was related to some biochemical parameters (oil quality).  The application of these recommendations in desert areas can play a role in reducing the food gap for edible oil in Egypt.