Sugarcane grown under a wide range of agro-climatic conditions accounts for ~80% of the sugar production worldwide. Since sugarcane productivity is severely affected by abiotic stresses and hence, an experiment was conducted for two consecutive years during 2020 and 2021 on popular sub-tropical sugarcane varieties. The experiment was laid out in two-factorial RBD consisting of nine sugarcane genotypes (Co 98014, Co 0118, Co 0238, Co 05011, Co 06034, Co 09022, Co 12029, Co 15023 and Co 15027) and salinity treatments (Control, ECiw ~4, 8 and 12 dS m−1) in 5 replications. Two budded setts were planted in pots and irrigated with saline water of respective levels till formative phase and observed the build-up in electrical conductivity of soil extract (ECse) from 0.48 (control) to 2.99, 4.81 and 7.08; while further saline irrigation increased the ECse values to 4.48, 6.24 and 9.33 dS m−1 in treatments ECiw ~4, 8 and 12 dSm−1, respectively. Increase in soil EC decreased plant survival by 24.1, 47.0 and 79.6% under continued irrigation of ECiw ~4, 8, 12 dS m−1 with respect to control. Continued saline irrigation caused significant reduction in growth, which was associated with reduction in relative water content (RWC) and gas exchange traits. RWC decreased by 4.91 to 21.9%, chlorophyll content by 8.46 to 32.75%, photosynthetic rate (Pn) by 16.85 to 91.44%, stomatal conductance by 14.96 to 84.25%, transpiration rate by 14.13% to 89.8% and chlorophyll fluorescence by 5.33 to 42.67% from ECiw ~4 to 12 dS m−1, respectively. Significant variations in Na+ and K+ ion content was observed under elevated saline condition in roots, leaves and juice extract of genotypes. Na+/K+ ratio, an important trait for screening salinity tolerance, increased in all genotypes as compared to control, the increase was predominant in susceptible varieties. Single cane weight (SCW) was drastically affected by saline irrigation, with a reduction of 36.4, 68.5 and 83.5% at ECiw ~4, 8 and 12 dS m−1, respectively as compared to control, with similar declining trend in juice quality. Based on our results, Co 0238, Co 0118 and Co 98014 were tolerant to salinity stress by maintaining higher Pn, lower leaf Na+/K+ ratio, higher SCW and higher juice sucrose content.