In saline conditions, establishing healthy seedlings is crucial for the productivity of sunflowers (Helianthus annuus L.). Excessive potassium (K+) from irrigation water or overfertilization, similar to sodium (Na+), could adversely affect sunflower growth. However, the effects of salt stress caused by varying K/Na ratios on the establishment of sunflower seedlings have not been widely studied. We conducted a pot experiment in a greenhouse, altering the K/Na ratio of a soil solution to grow sunflower seedlings. We tested three saline solutions with K/Na ratios of 0:1 (P0S1), 1:1 (P1S1), and 1:0 (P1S0) at a constant concentration of 4 dS m−1, along with a control (CK, no salt added), with five replicates. The solutions were applied to the pots via capillary rise through small holes at the bottom. The results indicate that different K/Na ratios significantly influenced ion-selective uptake and transport in crop organs. With an increasing K/Na ratio, the K+ concentration in the roots, stems, and leaves increased, while the Na+ concentration decreased in the roots and stems, with no significant differences in the leaves. Furthermore, an excessive K/Na ratio (P1S0) suppressed the absorption and transportation of Mg2+, significantly reducing the Mg2+ concentration in the stems and leaves. A lower leaf Mg2+ concentration reduced chlorophyll concentration, impairing photosynthetic performance. The lowest plant height, leaf area, dry matter, and shoot/root ratio were observed in P1S0, with reductions of 27%, 48%, 48%, and 13% compared to CK, respectively. Compared with CK, light use efficiency and CO2 use efficiency in P1S0 were significantly reduced by 13% and 10%, respectively, while water use efficiency was significantly increased by 9%. Additionally, improved crop morphological and photosynthetic performance was observed in P1S1 and P0S1 compared with P1S0. These findings underscore the critical role of optimizing ion composition in soil solutions, especially during the sensitive seedling stage, to enhance photosynthesis and ultimately to improve the plant’s establishment. We recommend that agricultural practices in saline regions incorporate tailored irrigation and fertilization strategies that prioritize optimal K/Na ratios to maximize crop performance and sustainability.