Subsurface drainage and organic fertilizer application are two important measures for improving saline–alkali soils, while the effects of different drainage spacings combined with organic fertilizer application amounts on alfalfa growth and coastal saline soil properties have seldom been evaluated. This study designed subsurface drainage pipes at four spacing distances, including 0 m (CK, without subsurface drainage), 6 m (S1), 12 m (S2), and 18 m (S3), and three organic fertilizer application amounts, including 3000 kg/ha (N1), 4500 kg/ha (N2), and 6000 kg/ha (N3), to observe the effects of different combinations of subsurface pipe spacings and organic fertilization amounts on alfalfa yield, quality, soil salinity, and nutrients. The results showed that the yield of alfalfa increased with higher fertilization amounts and smaller spacing between drainage pipes. The highest yield occurred in the S1N3 treatment, and the three batches reached 1268.5 kg/ha, 3168.0 kg/ha, and 2613.3 kg/ha, respectively, significantly (p < 0.05) higher than CK for all three batches. The increase in organic fertilizer amount resulted in an increase of 0.5–9.3% in the crude protein content, a decrease of 1.8–3.4% in the neutral detergent fiber content, and a decrease of 1.3–5.5% in the acid detergent fiber content for alfalfa plants. Under CK, the contents of quality indicators in alfalfa were the highest. For the drainage treatments, the quality indicator contents were overall at a higher level under S3. Subsurface drainage had a reduction effect on the salinity of all the 0–80 cm soils. For the surface soil, it was detected that smaller spacing was beneficial for reducing soil salt content, while higher fertilization amounts increased the salt content. S1 reduced the soil salt content by 36.3–46.1% compared to CK; however, N3 increased the salt content by 7.0–16.2% compared to the other two fertilization treatments. In addition, smaller spacing between the subsurface drainage pipes generally reduced the soil’s available nitrogen, and total nitrogen increased the C/N ratio but had no significant effect on the organic matter. It was concluded that the spacing between subsurface drainage pipes and the application amounts of organic fertilizer have remarkable impacts on alfalfa yield and quality, mainly by changing the soil salinity and nutrient status.