Initial fluctuation is one of the ingredients that washes fingerprints of the nuclear symmetry energy on observables in heavy-ion collisions. By artificially using the same initial nuclei in all collision events, the effect of the initial fluctuation on isospin-sensitive observables, e.g., the yield ratio of free neutrons with respect to protons Nn/Np, 3H/3He yield ratio, the yield ratio between charged pions π−/π+, and the elliptic flow ratio or difference between free neutrons and protons v2n/v2p (v2n-v2p), are studied within the ultrarelativistic quantum molecular dynamics (UrQMD) model. In practice, Au + Au collisions with impact parameter b = 5 fm and beam energy Elab = 400 MeV/nucleon are calculated. It is found that the effect of the initialization on the yields of free protons and neutrons is small, while for the yield of pions, the directed and elliptic flows are found to be apparently influenced by the choice of initialization because of the strong memory effects. Regarding the isospin-sensitive observables, the effect of the initialization on Nn/Np and 3H/3He is negligible, while π−/π+ and v2n/v2p (v2n-v2p) display a distinct difference among different initializations. The fingerprints of symmetry energy on π−/π+ and v2n/v2p can be either enhanced or reduced when different initializations are utilized.