您需要手动调用dx eg。

task finalize() {
    doFirst {
        println('Encrypting!')
        println("${projectDir}")
        exec {
            workingDir "${projectDir}/build/intermediates/classes/debug"
            commandLine "/home/MyUser/Android/Sdk/build-tools/26.0.0/dx"             \
            , "--dex"             \
            , "--output=my/example/com/secureme/SecuredData.dex"             \
            , "my/example/com/secureme/SecuredData.class"
        }
        //We don't want in our APK this .class
        project.delete "build/intermediates/classes/debug/my/example/com/secureme/SecuredData.class"
        // Encrypt our .dex file
        encrypt.execute()
        copy {
            from "build/intermediates/classes/debug/my/example/com/secureme/SecuredData.dex"
            into "src/main/assets/"
        }
    }
}
tasks.withType(JavaCompile) { compileTask -> compileTask.finalizedBy finalize }

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完整示例here