Multiple time scales are the intrinsic nature of complex systems and can be revealed through single molecule photon statistical analysis. The standard Poisson indicator defined by the time-averaged initial condition measures photon bunching and antibunching but cannot be directly related to multiple time scales. A new indicator defined by the event-averaged initial condition is proposed to detect the deviation from the renewal behavior and to directly probe the effects of conformational fluctuations. Detailed calculations of modulated two-level systems are carried out using the transfer matrix method to demonstrate the difference between the two indicators. The relationship between ensemble-averaged survival probabilities and photon statistics is also explored in the context of single molecule measurements.