We report technique used for improved measurement uncertainties for Photon detection efficiency(PDE) of $1mm^2$ single pixel SiPM. It consists of 470nm LED light source, two 2-inch integrating sphere and two NIST calibrated silicon photodiodes that have ${pm}2.4%$ calibration error. With raytracing simulation of our experimental setup, we predict number of photon into SiPM and measurement uncertainty. For MPPC, Hamamatsu suggested PDE(1600 micro pixel) including crosstalk and afterpulse is 23.5% at 470 nm. By using new low calibration error photodiode and raytracing simulation, our simulation result has ${pm}3%$ measurement uncertainty. The technical detail of measurement, simulation are presented with the results and implication.