The exercises come at a time of heightened tension in the contested waters after an arbitration court in the Hague ruled this month that China did not have historic rights to the South China Sea and criticised its environmental destruction there.
China rejected the ruling and refused to participate in the case.
"This is a routine exercise between the two armed forces, aimed at strengthening the developing China-Russia strategic cooperative partnership," China's defense ministry spokesman Yang Yujun told a regular monthly news conference.
"The exercise is not directed against third parties."
China and Russia are veto-wielding members of the UN Security Council, and have held similar views on many major issues such as the crisis in Syria, putting them at odds with the United States and Western Europe.
Last year, they held joint military drills in the Sea of Japan and the Mediterranean.
China claims most of the South China Sea, through which more than $5 trillion of trade moves annually. Brunei, Malaysia, the Philippines, Taiwan and Vietnam have rival claims.
China has repeatedly blamed the United States for stoking tension in the region through its military patrols, and of taking sides in the dispute.
The United States has sought to assert its right to freedom of navigation in the South China Sea with its patrols and denies taking sides in the territorial disputes.
Russia has been a strong backer of China's stance on the arbitration case, that was brought by the Philippines.
Yang said China and Russia were comprehensive strategic partners and had already held many exercises this year.
"These drills deepen mutual trust and expand cooperation, raise the ability to jointly deal with security threats, and benefit the maintenance of regional and global peace and stability," he said.
