"All we have to do is stop hunting endangered spices....." I had been thinking that, this sentence has no problem at all and seems so natural. But suddenly as I come across that " is + verb + gerund" again, I'm little confused because there should be a gerund or noun, instead. Is "stop hunting" part considered as clause or something? I feel like I'm lost.
I don't care much about terminology as such, but in the context of OP's example there are two possible interpretations - which you might find it helpful to distinguish between by calling them "true verb" and "gerund" usages. It might also help to consider things using a slightly different sentence...
The Prime Minister promised to stop hunting foxes.
If we understand hunting there as a verb usage (syntactically, the most likely situation), the implied subject of the verb is the PM (i.e. - he promised that he will no longer engage in hunting himself).
If we understand it as a gerund usage, it refers to fox-hunting as an activity (by implication, carried out by other unspecified people), which is semantically the most likely intended meaning. The PM promised that he will stop/prevent other people (everyone) from indulging in the practice (i.e. - he will ban fox-hunting).
In OP's exact context, it's really a matter of opinion which interpretation to apply. Probably the advice isn't specifically addressed to the relatively small number of people who actually do hunt endangered species (it's highly unlikely the writer includes himself in that group, which would be implied by the use of we).
The most natural interpretation is that the writer is using we to mean humankind in general, and that he's advising "us" collectively to stop / cease / abstain / refrain from hunting (i.e. - each of us should voluntarily change our behaviour if we we are hunters).
The "contrived" interpretation is that we're being urged to act collectively to bring an end to such hunting (by voting in politicians who will introduce laws to ban the practice, perhaps).
Verb+Gerund also functions as a infinitive clause, it has no explanation, just that there are some verbs that -ing will always replace 'to', and it's obligatory, it's a rule, here are some verbs that don't take the preposition 'to' but the '-ing'.
He stopped looking at me as soon as I turned around
He started talking to me although I didn't even know him
I advise her drinking more tea
The thief admitted breaking into the house
I have avoided talking to her
I began learning English.
More examples, you can check out this list containing all the verbs that must be followed by gerund: