An Internet of Things (IoT) networking authentication system and a method thereof are provided. The IoT networking authentication system includes an idle IoT apparatus and a networked IoT apparatus. The idle IoT apparatus encrypts a connection request according to a key to generate a connection request ciphertext and sends the connection request ciphertext. The networked IoT apparatus receives the connection request ciphertext and decrypts, according to the key, the connection request ciphertext to obtain the connection request. The networked IoT apparatus authenticates the idle IoT apparatus according to the connection request to generate an authentication result. The networked IoT apparatus determines, according to the authentication result and a networking condition, whether to allow the idle IoT apparatus to join an IoT network, so as to generate a connection response. The networked IoT apparatus outputs the connection response to the idle IoT apparatus.