Are the Imperials allied with the Thalmor?

I've completed the main quest in Skyrim, and now i'm wondering which side to join in the civil war.

Is it true that Empire is allied with Thalmor?

If it is, then I'll join Ulfric Stormcloak's rebels.

It's a bit more complicated than allied...

The short version is this: A few years back, there was a massive war between the Empire, and the Aldmeri Dominion, the latter is a kingdom of Elves, in which the Thalmor are basically the government, the army, the secret police, and the mages guild all rolled into one.

The Empire lost. Badly. The treaty that was signed to put an end to the war included a number of terms which were less than favorable to the Empire. Among them were the outlawing of Talos-worship throughout the Empire, and the allowing of Thalmor ambassadors, mages, and soldiers to inspect Imperial lands, and ensure that the terms of the truce were being adhered to.

So, while it's true that the Empire isn't actively at war with the Thalmor, and indeed, the fact that the Empire allows the Thalmor to wander about Skyrim killing Talos worshippers is one of Ulfrics primary grievances, calling the two allies is something of a stretch.

Indeed, if you end the Civil War on the Imperial side of things, General Tulius will remark

that the Empire will never be able to fight back against the Thalmor unless they can deal with and shut down various rebellion's like Ulfrics. And that once that's done, it will be time to deal with them.

Meanwhile, if you follow the Main Quest, at one point you'll get to raid the Thalmor Embassy and read their logs. Among other things, you'll learn that

Ulfric is essentially an 'agent' of the Thalmor. He may not actually be in service to them, but his rebellion is all a part of their plan - his Talos worship is the justification they need to return to war with the Empire in the future, and the rebellion itself weakens and fragments the Empire, making them easier prey in a future war of conquest.

When the Thalmor Dossier about Ulfric Stormcloak is found, it states that if either side wins the Civil War it would negatively affect the Thalmor's goals; they claim that an ideal situation would be a long war in which neither side truly "wins".

So regardless who you support on the civil war if you put on end to it while siding to the Imperials or the stormcloaks you will put across the Thalmor.