When the EPS file is created, is that font being embedded into the EPS? That should solve the problem.
yes the font is not getting embedded in eps. Is it because mathtype does not support the font? but it is been viewed in mathtype.
The STIX fonts are OTF, which MathType does not fully support. Some of the glyphs within the font will be visible in MT and usable in equations, but the full character set will not be. There may also be other issues, which you've noticed. If you're able to save the equation as PDF rather than EPS, the STIX font symbols should display in ID. (On the Mac, you can save directly as PDF within MathType. If you're on Windows, you can use the Adobe PDF printer. The result should be the same.)