The adsorption and self-assembly of meso-tetra(p-methoxyphenyl)porphyrinatocobalt(II) [Co(TAP)] on Au(111), Ag(111) and Cu(111) have been systematically studied by ultrahigh vacuum low-temperature scanning tunneling microscopy (STM). The atomically flat metal substrate surfaces are prepared by cycled ion sputtering and subsequent annealing at 750 K. Co(TAP) molecules are deposited onto the substrate surfaces via thermal evaporation from a home-made tantalum boat. The as-prepared samples are then annealed to achieve energetically stable self-assembly structures and transferred to the STM chamber for further analyses. All STM measurements are carried out at about 4.4 K. On these metal surfaces, Co(TAP) molecules mainly form two types of two-dimensional molecular assembly structures A and B. Structure A only exists on Au(111) and Ag(111), while Structure B merely appears on Ag(111) and Cu(111). The intermolecular interactions in Structures A and B are due to π-π stacking and hydrogen bonding, respectively. The difference in strength of the molecule-substrate interaction, which induces conformational changes of peripheral p-methoxyphenyl substituent in Co(TAP) on difference substrate, is attributed to govern the formation of different self-assembly structures on the aforementioned surfaces. The substrate surface also has an effect on the formation of the self-assembly structures. At similar coverage, the percentage of dispersed Co(TAP) molecules follow the sequence: Cu(111)>Au( 111)>Ag(111). With the coverage increase, the percentage of dispersed Co(TAP) molecules decreases on all metal surfaces employed in this study. Specifically, on Au(111) and Ag(111), the dispersed Co(TAP) molecules disappear at coverages of about 1 ML and 0.1 ML, respectively, while on Cu(111) they survive even at the coverage of about 0.85 ML. In addition, Structure A gradually dominates on Au(111). On Cu(111), Structure B only occupies half of the surface structures even at nearly saturated coverage. The ratio of Structures A to B almost retains over the whole coverage range on Ag(111). Thermal annealing of the molecule-covered Ag(111) substrate helps the transformation from Structure B to A, and the elimination of the structural domain boundaries as well.