We study the thermodynamics of the large N noncommutative super Yang-Mills theory in the strong 't Hooft coupling limit in the spirit of the AdS-CFT correspondence. It has already been noticed that some thermodynamic quantities of near-extremal D3-branes with NS B fields, which are dual gravity configurations of the noncommutative N = 4 super Yang-Mills theory, are the same as those without B fields. In this paper, (1) we examine the alpha'R-3(4) corrections to the free energy and find that the part of the tree-level contribution remains unchanged, but the one-loop and the nonperturbative D-instanton corrections are suppressed, compared to the ordinary case. (2) We consider the thermodynamics of a bound state probe consisting of D3-branes and D-strings in the near-extremal D3-brane background with B fields, and find that the thermodynamics of the probe is the same as that of a D3-brane probe in the D3-brane background without B fields. (3) The stress-energy tenser of the noncommutative super Yang-Mills theory is calculated via the AdS-CFT correspondence. It is found that the tenser is not isotropic and its trace does not vanish, which confirms that the super Yang-Mills theory is not conformal even in four dimensions due to the noncommutative nature of space. Our results render further evidence for the argument that the large N noncommutative and ordinary super Yang-Mills theories are equivalent not only in the weak coupling limit, but also in the strong coupling limit.