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Intercropping is extensively used to increase land productivity and agricultural benefits. In developing countries, intercropping has historically been one of the most widely used cropping systems. Crop models have been used to assess risk productivity over time and space, particularly in monocropping systems. Crop models, such as the Decision Support System for Agrotechnology Transfer (DSSAT), have been widely used to improve crop growth, development, and yield predictions; however, this model has some limitations when assessing interspecific competition in intercropping systems (e.g., it does not have a subroutine capable of running two crops simultaneously). Therefore, in this study, we developed a new approach to allow DSSAT to run two crop species in intercropping systems. A light interception algorithm and modified source code were integrated into the DSSAT to simulate the relay-strip intercropping system. The intercrop model developed in this study is the first intercrop model for DSSAT. This model is generic and can be employed to build other cereal–legume intercrop models for DSSAT Version 4.8. Regarding risk assessment of crop production, the model can evaluate long-term cereal–legume intercrop yields in low-input cropping systems. Therefore, before officially launching the new model in DSSAT, more field trials are recommended to rigorously evaluate and improve the model with data from different environments. The intercrop model developed in this study is simple, so this modeling approach can be employed to develop other cereal–noncereal intercrop models.