The anisotropy caused by columnar β grains are the main challenges in arc additive manufacturing of Ti-6Al-4V. In order to handle these issues, multilayer walls are deposited with different pulse frequencies and heat inputs. Combined with finite element analysis, the influence of pulse frequency and heat input on macrostructure and microstructure of deposited Ti-6Al-4V compounds are investigated. Results indicate that with the increase of pulse frequency, the widths of deposited walls decrease rapidly at first, then increase slightly; columnar β grains transform into equiaxed β grains and the grains get finer, but α phases have no obvious variation. The increasing heat input is beneficial to obtaining equiaxed β grains, but the wall width will enlarge and α phases will be coarser. The width of the specimen is determined by the dimension of the molten pool, which is influenced by the average heat input and the input heat in peak time period. Improving pulse frequency can break the dendrites as well as reduce the temperature gradient, which is conducive to the nucleation. Besides, higher heat input can reduce the temperature gradient as well. Therefore, equiaxed β grains are formed with the increase of pulse frequency and heat input. The morphology of α phases are mainly associated with the cooling rate. Reducing heat input can increase cooling rate and refine α phases.