We have studied the nucleon structure functions $F_{iN}^{EM} (x,Q^2);~i=1,2$, by including contributions due to the higher order perturbative QCD effect up to NNLO and the non-perturbative effects due to the kinematical and dynamical higher twist (HT) effects. The numerical results for $F_{iN}^{EM}(x,Q^2)$ are obtained using Martin, Motylinski, Harland-Lang, Thorne (MMHT) 2014 NLO and NNLO nucleon parton distribution functions (PDFs). The dynamical HT correction has been included following the renormalon approach as well as the phenomenological approach and the kinematical HT effect is incorporated using the works of Schienbein et al. These nucleon structure functions have been used as an input to calculate the nuclear structure functions $F_{iA}^{EM} (x,Q^2)$. In a nucleus, the nuclear corrections arise because of the Fermi motion, binding energy, nucleon correlations, mesonic contribution, shadowing and antishadowing effects. These nuclear corrections are taken into account in the numerical calculations to obtain the nuclear structure functions $F_{iA}^{EM} (x,Q^2)$, for the various nuclear targets like $^{12}C$, $^{27}Al$, $^{56}Fe$, $^{64}Cu$, $^{118}Sn$, $^{197}Au$ and $^{208}Pb$ which are of experimental interest. The effect of isoscalarity correction for nonisoscalar nuclear targets has also been studied. The results for the $F_{iA}^{EM} (x,Q^2)$ are compared with nCTEQ nuclear PDFs parameterization as well as with the experimental results from JLab, SLAC and NMC in the kinematic region of $0.1 \le x \le 0.8$ for several nuclei.