"Russia seeks to make a desert and call it peace," he said of the country's bombing of Aleppo, Sky News reported.
"The human tragedy is heart-breaking," he added.
"I believe the Russian conduct in Syria, allied with that of Assad's discredited regime, will, if they do not change course, provide a tragic example of the perils of forfeiting legitimacy.
"In defining as a terrorist anyone who opposes a brutal government, they alienate precisely that group that has to be on side if the extremists are to be defeated."
Younger, who is known within the organisation as 'C', gave the speech to an invited audience of journalists.
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He said: "The facts on the ground are staggeringly complex. The plight of Syrians continues to worsen. I cannot say with any certainty what the next year will bring.
"But what I do know is this: we cannot be safe from the threats that emanate from that land unless the civil war is brought to an end."
Younger is a career spy, having joined MI6 in 1991 after a short stint in the British Army.
He spent time working in the Middle East and Afghanistan and was involved in the security for the 2012 London Olympics.
His speech, as rare as it was wide-ranging, also made reference to the close working relationship with U.S., French and German Intelligence.
He specifically addressed the effect of Brexit and President-elect Trump, seeming to caution politicians against using security as a bargaining chip to negotiate Britain's exit from the EU.