The directional optical transmission characteristics of on-chip integrated optical isolators have wide applications in fields such as optical communication and optical signal processing. At early stage, various schemes of on-chip optical isolators have been developed, such as single-crystal magneto-optical pomegranate scheme, and silicon nitride (Si₃N₄) micro-ring resonators. However, there is still lack of compact on-chip optical isolator solutions. Here, a compact and integrated silicon optical isolator on a standard silicon on insulator (SOI) substrate is proposed and designed by intelligent algorithms and a variety of micro-nano circular vias. A modified genetic algorithm is developed, a segmented design fitness function is induced, and a gene library is established to obtain an ultra-compact optical isolator scheme with a size of only 4.2 μm×3 μm. On a standard silicon on insulator substrate, a linear passive isolation scheme is achieved by etching circular holes with five different diameters: 60 nm, 120 nm, 180 nm, 240 nm, and 300 nm. In the TE polarization mode, the design achieves an isolation degree of approximately 31 dB and an insertion loss of about 2 dB. Furthermore, in TM polarization mode, the design achieves an isolation degree of approximately 38 dB and an insertion loss of 2 dB; Finally, the influence of different size groups on the performance of isolators is analyzed. The results show that the smaller the circular hole structure, the better the isolation performance is. However, at the same time, we also need to consider the real silicon etching process requirements. In practice, holes that are too small are difficult to etch the effects of etching penetration at 10 nm, 20 nm and 30 nm between circular vias on the performance of the isolator are also evaluated, and the preliminary results show that the etching penetration caused by the more mature 30 nm etching process is acceptable. Therefore, considering all factors, it is recommended that the minimum circular hole size be 30 nm and the minimum distance adjacent circular holes be 30 nm. These results can promote the development of highly integrated and ultra-small on-chip optical signal directional transmission schemes.