Series of field experiments were conducted to evaluate the long term effect of gypsum and crop residue on crop yield and soil health in rice-wheat crop rotation system in salt affected soil. A saline-sodic field having $EC_e$ (electrical conductivity of the saturation extract) 4.77 ($dSm^{-1}$); pH ($H_2O$) 8.96; SAR 43.78 ($mmol;L^{-1}$) and gypsum requirement (G.R.) 2.86 (Mg $acre^{-1}$) was selected on Soil Salinity Research Institute Farm. Five treatments consisting of ($T_1$) control, ($T_2$) gypsum at 100% G.R., ($T_3$) gypsum at 25% G.R. + wheat straw at $3Mg;ha^{-1}$, ($T_4$) gypsum at 25% G.R. + rice straw at $3Mg;ha^{-1}$, ($T_5$) gypsum at 25% G.R.+ rice and wheat straw at $3Mg;ha^{-1}$ were replicated four times under completely randomized block design. The data indicated that grain and straw yield of rice and wheat was significantly (P<0.05) increased by all the amendments used either single or in combination. $T_2$ (gypsum at 100% G.R.) significantly (P<0.05) increased grain and straw yield of rice and wheat crops followed by $T_3$ (gypsum at 25% G.R. + wheat straw at $3Mg;ha^{-1}$) when compared with control. Soil properties were also improved by used amendments, pronounced decreased in $EC_e$, $pH_s$ and SAR were recorded in $T_2$ followed by $T_3$. The efficiency of the treatments could be arranged in following order gypsum at 100% G.R.> gypsum at 25% G.R. + wheat straw at $3Mg;ha^{-1}$ > gypsum at 25% G.R. + rice and wheat straw at $3Mg;ha^{-1}$ > gypsum at 25% G.R. + rice straw at $3Mg;ha^{-1}$ > control.