We study the transverse momentum ( $p_T$ ) differential anisotropic flow and flow fluctuation in Pb+Pb collisions at $\sqrt{s_{_{NN}}}$ =5.02 TeV at the LHC. A (3+1)-dimensional CLVisc hydrodynamics framework with fluctuating TRENTO (or AMPT) initial conditions is utilized to simulate the space-time evolution of the quark-gluon plasma (QGP) medium. The effects of shear viscosity and the sub-nucleon structure on anisotropic flow and flow fluctuation are analyzed. Our result shows that shear viscosity tends to suppress both flow coefficients ( ${v_2\{2}\}$ , ${v_2\{4\}}$ , and ${\langle v_2\rangle}$ ) and flow fluctuation ( ${\sigma_{v_2}}$ ) owing to its smearing effect on local density fluctuation. The flow coefficients appear to be insensitive to the sub-nucleon structure, whereas the flow fluctuation ${\sigma_{v_2}}$ tends to be suppressed by the sub-nucleon structure in central collisions but enhanced in peripheral collisions. After taking into account the sub-nucleon structure effect, our numerical result can qualitatively describe the relative flow fluctuations ( ${v_2\{4\}/v_2\{2\}}$ , $F({v_2})$ ) measured by the ALICE Collaboration at the LHC. We further investigate the effects of shear viscosity, sub-nucleon structure, and initial condition model on the flow angle and flow magnitude decorrelations ( ${A_2^f}$ , ${M_2^f}$ ) using the four-particle correlation method. We find that the flow decorrelation effect is typically stronger in central collisions than in peripheral collisions. The flow angle decorrelation is found to be insensitive to the shear viscosity and sub-nucleon structure, whereas the flow magnitude decorrelation shows quite different behaviors when using the TRENTO and AMPT initial condition models. Our study sheds light on the anisotropic flow, transport properties, and initial structure of the QGP created in high-energy nuclear collisions.