The decision, announced by prosecutors in Puerto Princesa on Palawan island, is set to further stoke the simmering territorial dispute in the South China Sea.
Prosecutor Allan Ross Rodriguez told AFP he would file charges in court later Monday, rejecting the appeals of two Chinese diplomats who met him earlier in the day about the case.
"It is clear: there was a fishing vessel, Chinese fishermen, a catch of (protected) sea turtles. It is clear from what the apprehending officers said," Rodriguez said, explaining the basis for his decision.
Chinese embassy officials in Manila could not be contacted for comment.
Filipino police seized the Chinese-flagged vessel and detained its 11 crew last week off disputed Half Moon Shoal.
However, two were found to be minors and would be repatriated without charges, Rodriguez said.
The remaining nine would be charged with violating laws against poaching and catching protected species.
If found guilty of collecting "rare, threatened or endangered" species, the most serious allegation, they could face up to 20 years in prison and large fines.
Poaching in Philippine waters itself is punishable by fines of up to $200,000.
Filipino police said they found a huge haul of hundreds of sea turtles -- a protected species -- on board the 15-tonne vessel, many of them already dead.
China has demanded that the Philippines free the fishermen immediately, saying it has "undisputable sovereignty" over the shoal.
Its foreign ministry and embassy in Manila have also urged the Philippines to "stop taking further provocative action" that would harm relations.
Rodriguez said the Philippine government has assigned lawyers to represent the crewmen after the Chinese diplomats declined to hire defence lawyers.
Half Moon Shoal is 111 kilometres (60 nautical miles) west of Palawan, the most westerly island in the Philippines. It is located on the eastern edge of the Spratlys, a chain that sits near vital sea lanes and is believed to harbour vast oil and gas resources.
China's claim to nearly all of the South China Sea has strained its ties with Southeast Asian countries.
Last week Vietnam accused China of ramming its ships in an encounter near another disputed territory in the sea.
Leaders of the Association of Southeast Asian Nations, which includes both Vietnam and the Philippines, in a statement after a weekend summit expressed "serious concern" at the maritime disputes.
China's extensive claims also overlap those of Asean members Brunei and Malaysia, as well as Taiwan's.
The Philippines in March filed a formal plea to the United Nations challenging Beijing's claims, in defiance of Chinese warnings that it would seriously damage their already frayed relations.
Beijing has rejected UN arbitration and urged Manila to settle the dispute through bilateral talks instead.