We report a new and improved photon counting method for the precision PDE measurement of SiPM detectors, utilizing two integrating spheres connected serially and calibrated reference detectors. First, using a ray tracing simulation and irradiance measurement results with a reference photodiode, we investigated irradiance characteristics of the measurement instrument, and analyzed dominating systematic uncertainties in PDE measurement. Two SiPM detectors were then used for PDE measurements between wavelengths of 368 and 850 nm and for bias voltages varying from around 70V. The resulting PDEs of the SiPMs show good agreement with those from other studies, yet with an improved accuracy of 1.57% (1σ). This was achieved by the simultaneous measurement with the NIST calibrated reference detectors, which suppressed the time dependent variation of source light. The technical details of the instrumentation, measurement results and uncertainty analysis are reported together with their implications.