The directive comes as anti-government protests in Hong Kong threaten the status of the Asian financial hub.
Hong Kong, one of the world's busiest ports, is on the verge of its first recession in a decade as violent anti-government protests scare off tourists and bite into retail sales and investment.
The State Council 19-point directive, published in state-media outlet People's Daily, calls for Shenzhen's "economic strength and development" to rank among the best in the world by 2025, and a "global benchmark" by the middle of the century.
In the 1990s, market-oriented reforms and government support transformed Shenzhen from an ordinary Chinese village to a major hub for China's manufacturing and technology sectors.
The city now houses the global headquarters for Tencent, China's social media giant, and Huawei, the networking equipment maker that U.S. President Donald Trump effectively barred U.S. companies from supplying.
The directive called for the "modernization of social governance" in Shenzhen via the "comprehensive application of big data, cloud computing, artificial intelligence and other technologies."
It called for the integration of the culture and economy of Shenzhen with Hong Kong and Macao via funding for hospitals, joint disaster relief efforts and cultural exchanges, and to further develop the Hong Kong-Macao Greater Bay Area and "enrich the new practice of the 'one country, two systems' policy."
Hong Kong returned from British to Chinese rule in 1997 under a "one country, two systems" formula that promised wide-ranging freedoms denied to citizens in mainland China, but many in the city believe Beijing has been eroding those freedoms.
Hong Kong's protests started as opposition to a now-suspended extradition bill to mainland China and have swelled into wider calls for democracy.
Last week China's paramilitary forces carried out exercises outside of a major sports stadium in Shenzhen, sparking speculation that they may be used in Hong Kong.