Fiber reinforced polymers (FRPs) have gained widespread application in civil engineering due to their light weight, high strength, and excellent corrosion resistance. Among various fibers, natural fibers have recently attracted increasing attention because of their renewability, low cost, and reduced environmental impact. However, natural fiber reinforced polymer composites (NFRPs) suffer from high moisture absorption and inferior mechanical properties, which are further deteriorated under hygrothermal environments, severely limiting their service conditions. This study focuses on flax fiber reinforced polymer composites (FFRPs) and, through systematic experimental testing, investigates their durability under hygrothermal conditions. Hygrothermal aging was conducted at 90% relative humidity and 40 °C for up to 30 days. Water uptake, mechanical properties, and thermomechanical behavior were evaluated for composites fabricated by two molding processes (autoclave and hand-laying) with varying ply numbers (10, 20, 30, 40, and 50 layers). The optimal ply number for mechanical performance was identified, and the influence of the different resin systems and fiber forms between the two processes on the cross-process comparison, as well as the rationale for the 30-layer laminate and the effect of laminate thickness, were clarified. Microstructural changes were examined via scanning electron microscopy. This work provides systematic experimental evidence and data for assessing the long-term durability of FFRP composites in humid and warm environments, offering valuable guidance for their practical application in civil infrastructure.