Habitat changes in marine ranching can cause variations in biological resources and community structure. However, the complex inter-domain ecological network (IDEN) in this particular habitat are not well understood. Thus, we employed field surveys and multivariate statistical analyses to explore the spatio-temporal heterogeneity and the IDEN of biological communities within a marine ranching in southern Yintan of Beihai City, China. Our findings indicated that seasonal succession and artificial reefs (ARs) deployment had simultaneous effects on both biotic and abiotic factors, and the former effect was more pronounced. Based on orthogonal partial least squares discriminant analysis (OPLS-DA), various biota (phytoplankton, zooplankton, and nekton) can be broadly categorized into four groups (BT, BC, AT, and AC) on seasonal and spatial scales. Variable importance projection (VIP) and redundancy analysis (RDA) demonstrated that autumn biomarkers such as Hemidiscus hardmannianus, Oikopleura rufescens, Lagocephalus lunaris etc. were positively correlated with WT, Sal and IN, whereas spring biomarkers such as Rhizosolenia robusta, Euconchoecia aculeata, Penaeus penicillatus etc. were positively correlated with DO, COD, and IP. The IDEN analysis revealed that 23 species including Chaetoceros densus, Centropages tenuiremis, Parargyrops edita etc., played a key role in maintaining the stability of the biological communities and realising the ecological functions in the studied sea area. This study can provide novel insights and theoretical supports for the ecological effects analysis and species protection in marine ranching.