Yes, if you have two moves of the same power but your Attack is higher than Special Attack, the physical one will have higher power. But it also depends on the opponent's Defense and Special Defense. If they have much higher Defense (e.g. Golem) then the physical attack might do less damage than the special one.
Here's a tip: multiply the power of the physical move by your Attack, and the power of the special move by your Special Attack. Whichever one is higher is going to hit with more power. (Note: the number you get is not the exact power but it's relative, i.e. if you get a number twice as big, it would hit with twice as much power.)
Example: Charizard with Atk=220, Sp.Atk=348 (max). And you are deciding between Flare Blitz and Flamethrower.
Flare Blitz = 120 x 220 = 26400
Flamethrower = 95 x 348 = 33060
So even though Flamethrower is less powerful, it hits harder than Flare Blitz (plus you don't get recoil with Flamethrower).