Soil salinity may limit plant growth and development, and cause yield loss in crop species. This study aimed at remediating saline soil using organic matter (OM) treatment, before the cultivation of RD6 rice (Oryza sativa L. spp. indica). Physiological and morphological characters of rice plants, as well as crop yield, were evaluated from salt-affected soil with varying levels of salinity. The chlorophyll a and total chlorophyll pigments of rice plants grown in salt-affected soil (2% salt level) with the application of OM were maintained better than in plants grown without OM treatment. The degree of reduced photosynthetic pigments in rice plants was dependent on the level of salt contamination. Pigment content was positively related to maximum quantum yield of PSII (Fv/Fm) and quantum efficiency of PSII (ΦPSII), leading to reduced net photosynthetic rate (Pn) and reduced total grain weight (TGW). Photosynthetic abilities, including chlorophyll a and total chlorophyll pigments and ΦPSII, in rice plants grown with OM treatment were greater than in those cultivated in soil without the OM treatment, especially in high salt levels (1-2% salt). The remediation of salt-affected soil in paddy fields using OM should be applied further, as an effective way of enhancing food crop productivity.