The present invention provides a method and system for automatic verification of automatically generated standalone code intended for execution on a target computing platform against its original design simulated in a simulation environment. The present invention also applies to execution comparisons between two implementations, such as two simulations, one simulation and one standalone code implementation, or two standalone code implementations. Block diagrams can be used to create a comparison model that compares two implementations. The comparison of different implementations can be performed at a block level, a subsystem level, a model level, or multi-model level. The present invention allows automatic comparison once a user supplies the intermediate outputs and/or signals that the user wants to compare and monitor. Reports can be generated to show the statistics of the comparison results.