We analyze charmless two-body non-leptonic B decays $B \to PP, PV$ under the framework of factorization assisted topological amplitude approach, where $P(V)$ denotes a light pseudoscalar (vector) meson. Compared with the conventional flavor diagram approach, we consider flavor $SU(3)$ breaking effect assisted by factorization hypothesis for topological diagram amplitudes of different decay modes, factorizing out the corresponding decay constants and form factors from non-factorization (factorization) topological amplitudes after parameterizing (factorized in factorization framework) it as associated magnitude $\chi$ and strong phase $\phi$ (effective Wilson coefficient). These non-perturbative parameters are universal that can be extracted from current abundant experimental data of $B \to PP,PV$ simultaneously. With these best fitted parameters, we predict branching fractions and $CP$ asymmetries of 97 decay modes, which are in good agreement with measured data or to be test in the LHCb and the Belle-II experiments in the future. The long-standing $\pi \pi$ and $\pi K$-$CP$ puzzles are resolved with favorable color-suppressed tree emission diagram $C$.