Strategies for improving table grape quality under protected conditions are worth discussing. Two grape cultivars Baoguang (BG) and Cuiguang (CG) were used to evaluate the effects of trellis systems (pergola trellis and closing Y shaped trellis which defined as SAYM) and berry thinning intensities (high thinning intensity, HT; medium thinning intensity, MT; light thinning intensity, LT) on vine performance and quality composition under protected cultivation. Vines trained on the pergola trellis system had a higher budbreak rate of 81.79%, but a lower proportion (70.16%) of bearing shoots. Vines trained on the SAYM trellis system had a larger leaf area index (LAI) of 145.38 m2 m−2, but lower transmission coefficient (TC, 0.27), photosynthetically active radiation (PAR,160.73 μmol m−2 s−1), mean leaf angle (MLA, 19.88°) and transpiration rate (Tr, 3.82 mmol m−2 s−1). Water content and pulling resistance (PR) were lower in berries on the SAYM trellis or within heavily thinned (HT) clusters. HT promoted the remarkable improvement in total soluble solids (TSS), ratio of TSS to titratable acidity (TA), pH, sugar constituents, external color density and skin total anthocyanins, and most of these indexes were also enhanced by SAYM trellis. TA maintained low (4.51 g kg−1) on the pergola trellis and decreased with thinning intensity enhanced. Despite that, the effects of trellis and thinning intensity on organic acid constituents varied in cultivars. Nutrition elements mostly tended to accumulate in HT berries. Trellis systems were active in altering the texture attributes of BG. In addition, medium thinning (MT) and light thinning (LT) exerted similar effects on most tested attributes.