Forward osmotic membrane bioreactors (FOMBRs) have broad prospects for application in wastewater reuse and resource recovery. Problems such as concentration polarization, salinity accumulation, and membrane fouling have led to a rapid flux decline, which limit their practical application. In this study, we introduced aerobic granules into a FOMBR to clarify the effect of sludge morphology on reactor performance. The results showed that the average removal efficiency of total organic carbon (TOC) and phosphate-phosphorus (PO-P) were maintained above 95% during the operation of activated sludge-based FOMBR (R1) and aerobic granule-based FOMBR (R2), respectively. R2 achieved higher removal efficiency of ammonia–nitrogen (NH-N) with an average removal efficiency of 77%, which was significantly higher than R1 (57%). Over the entire operation, the content of the soluble microbial products (SMP) in R1 was generally higher than that in R2, which resulted in more polysaccharides and proteins in the fouling layer of the membrane. The membrane flux of R2 was 1.0 L·m·h higher than that of R1. The average size of flocs in R1 decreased from 137.24 μm to 76.84 μm, and that of the aerobic granules in R2 decreased from 2.35 mm to 1.20 mm and then remained stable. The results of microbial analysis showed that the membrane surface had lower microbial diversity than that of the mixed liquid, and the microorganisms enriched at the membrane surface were mainly Proteobacteria and Firmicutes with better salt tolerance.