If there is not bacteria in eye bacterial culture test, will the bacteria be in the inner surfaces of eye?

Usually not. If the culture is negative, you can be sure that bacteria are not a likely cause of a superficial eye infection, such as conjunctivitis. Some infections inside the eye could have a negative external culture, but if your doctor thought that is a possibility, you would be in the hospital and on IV antibiotics.

If your doctor did not draw fluid out of your eye with a needle to culture it, then your doctor does not suspect any bacterial infection inside the eye. If only the outside surface of your eye was swabbed and/or scraped for cultures, then your doctor has determined that your infection is limited to the external surface of your eye such as your conjunctiva or cornea. False negative cultures occur.