The couple, German nationals partially named as Xuejun C. and Hua S., were arrested in the southern city of Munich, said the federal prosecution service. It alleged that the pair "work for a Chinese intelligence agency".
Their homes and workplaces in Munich were being searched, along with other locations across Germany.
The couple are alleged to have "established contacts with numerous academics at German universities and research institutions, in particular with chairs in the fields of aerospace engineering, computer science and artificial intelligence".
To make these contacts, they were believed to have "posed as interpreters or as employees of an automobile manufacturer".
Some scientists were then "enticed to travel to China under the pretext of giving paid lectures to a civilian audience", but actually ended up addressing employees of state-owned arms manufacturers, prosecutors said.
As well as the suspects' arrests, prosecutors said that "further measures" were being carried out "concerning a total of 10 people who are not suspected of any offence but are potential witnesses" in Berlin, Munich and several other locations across the country.
According to the Handelsblatt daily, Xuejun C. is 55 years old and chairman of the German-Chinese Association for Technology, Education and Cultural Exchange in Munich.
He is believed to have close ties to a Chinese university that collaborates closely with German research institutions and that also maintains ties with Chinese defence research and industry, the daily said.
- 'Tip of iceberg' -
There have been a number of high-profile espionage cases in Germany linked to China recently.
In February a US citizen was jailed by a court in the western city of Koblenz for offering China sensitive information while working as a civilian contractor at a US military base.
In September a former aide to far-right politician Maximilian Krah was jailed for more than four years after a court found him guilty of acting as an agent for a Chinese intelligence service while working for Krah.
Prosecutors have also opened an investigation into Krah himself over allegations he took money from Russia and China during his time as a European parliamentarian, which he denies.
Earlier this week German Greens MP Konstantin von Notz, deputy chief of the intelligence oversight committee, warned of a growing threat from China.
"We are massively underestimating the energy and aggression with which China is acting against the West, including against Europe and Germany," he told a podcast by the Politico website.
Pointing to China's ties with Russia, he added that "autocrats have a common interest in forging alliances and sticking together against their supposed enemy", he said.
Centre-right CDU security expert Roderich Kiesewetter told Handelsblatt he feared the latest spy case "is just the tip of the iceberg, because China is proceeding very deliberately, with a very long-term perspective, and using a broad soft power network".