We present our results of the $K_{l3}$ form factors on the volume whose spatial extent is more than $L=$10 fm, with the physical pion and kaon masses using the stout-smearing clover $N_f = 2+1$ quark action and Iwasaki gauge action at $a^{-1}\approx2.3$ GeV. The $K_{l3}$ form factor at zero momentum transfer is obtained from fit based on the next-to-leading (NLO) formula in SU(3) chiral perturbation theory. We estimate systematic errors of the form factor, mainly coming from the finite lattice spacing effect. We also determine the value of $|V_{us}|$ by combining our result with the experiment and check the consistency with the standard model prediction. The result is compared with the previous lattice calculations.