I am a newcomer to ktor, I use the following for cookie management at client side,

private val cookieStorage: CookiesStorage = AcceptAllCookiesStorage()
    private val client = HttpClient(engine) {
        expectSuccess = true
        install(ContentNegotiation) {
            json(
                Json {
                    ignoreUnknownKeys = true
                    prettyPrint = true
                }
            )
        }
        install(HttpCookies) {
            cookieStorage
        }
    }

How can I manually clear the cookie stored by HttpCookies?

Unfortunately, you can’t.