A self-comparison method with closely interleaved switching states is analyzed and used to evaluate some type-B uncertainties of an Rb87 atomic fountain clock. Free from additional frequency reference, the method can be applied to a running fountain to reach a precision beyond its uncertainty. A verification experiment proves an uncertainty of 9.2×10 16 at an averaging time of 242500 s. Further, the method is applied to measure light shift, and no visible relative frequency shift is found in the fountain within the uncertainty of 2.1×10 15. When applied to the evaluation of a cold collisional shift, the result gives a 2.2×10 15 shift with a 9.5×10 16 uncertainty.