...he incests that he's fine

And we're off to a rollicking start.

My little brother, Spike, has been working to hard this past month.

Just say, Spike! There relationship, besides being friends and a team of two is all that needs to be said if no one ask. Especially in a story where, Twilight is a possible shipping.

And what is with to trains? Does no one use the chariot any more!

Dear, Princess Celestia.
My little brother, Spike, has been working to hard this past month. I keep telling him that he needs to take a break off, but he incests that he's fine, and that he can continue working. I know that he's not telling me the truth, and I feel that he's been working a lot more lately, than usual, but I can't figure out why.
So I was wondering, if Spike could stay in Canterlot with you and Luna, just for a few days, you know; like a vacation. Also, if you could, can you and Luna find out whats been bothering Spike, and whats been making him work so hard, please.
Sincerely, your loyal subject: Princess Twilight Sparkle.

The word is Insists

Incest is an unnatural relationship between family members.

Its kinda short but I can feel some sweetness in it.....

Dragon's in heat isn't he?

4767552 Pretty sure males don't go into heat.

You need to do a lot of editing to this story. At least you fix the mistakes pointed out to you, but those are few and the ones hidden are many...

4770401 u never know its a deferent species so male dragons might get in heat

4770401 Males can go into rut. I know bucks do.

I consider myself bad at punctuation; never knowing when exactly to use a comma, colon, semicolon, ellipsis, or whatever else.

But even my poor understanding knows that you don't use commas this much, nor in most of the places you've used them. You'd be better off erring on the side of not enough rather than too much.

It's not a perfect method, but putting in a line break at each place you think a comma goes gives you a more visual cue of how you're chopping things up.

Dear,
Princess Celestia.

Spike,
has been working very hard this past month.

I keep telling him that he needs to take a break off,
but he insists that he's fine,
and that he can continue working.

I know that he's not telling me the truth,
and I feel that he's been working a lot more lately,
than usual,
but I can't figure out why.

So I was wondering,
if Spike could stay in Canterlot with you and Luna,
just for a few days,
you know;
like a vacation.

Also,
if you could,
can you and Luna find out what's been bothering Spike,
and what's been making him work so hard,
please.

Sincerely,
your loyal subject:
Princess Twilight Sparkle.

You can see just how awkward many of those commas are this way. The one I know for absolute certain is your opener - the comma goes after the name and their should be a period, like this:

Dear Princess Celestia,

It'd be worthwhile to figure out what should go, what should stay, and what should be changed to a different bit of punctuation not only because it will make the reading of this story flow better, but also because of how it will help you write more clearly in the future.