An apparatus and method for enhancing security and stability in a heterogeneous computing environment that supports an open standard parallel program are provided. A method of enhancing security in a heterogeneous computing environment may include loading a source code kernel corresponding to an application program to be installed in a host system, determining whether the source code kernel is targeted for integrity check, based on a security policy of the host system, prior to cross-compiling the source code kernel, requesting a security engine of a computing device to check an integrity of the source code kernel, when the source code kernel is determined to be targeted for the integrity check, and controlling an operation of a runtime compiler based on a check result received from the security engine.