Co-occurrence of bacteria and microeukaryote species is a ubiquitous ecological phenomenon, but there is limited cross-domain research in aquatic environments. Here, we present a network statistical analysis and visualization of microbial cross-domain co-occurrence patterns based on DNA sampling of a typical subtropical bay during four seasons, using high-throughput sequencing of both 18S rRNA and 16S rRNA gene. First, we found obvious relationships between network stability and network complexity indices. For example, the increase of cooperation and modularity could weaken cross-domain networks stability. Second, we found that bacterial OTUs were the most important contributors to network complexity and stability, as they occupied more nodes, constituted more keystone OTUs, built more connections and, more importantly, ignoring bacteria led to greater variation in network robustness. Gammaproteobacteria, Alphaproteobacteria, Bacteroidetes and Actinobacteria were the most ecologically important groups. Finally, we found that the environmental drivers that best correlated with the cross-domain networks differ in different seasons (In detail, the network in January was primarily constrained by temperature and salinity, the network in April was primarily constrained by depth and temperature, the network in July was mainly affected by depth, temperature and salinity, depth was the most important factor affecting the network in October) and that environmental influence was stronger on bacteria than on microeukaryotes.