Inbreeding is thought to be a key adverse factor impacting the genetic quality of seeds in seed production populations and the inbreeding degree (i.e., selfing or outcrossing rate) of seed production populations have been extensively assessed through mating system analysis. The depression effect of inbreeding on seed quality traits in seed production populations under open-pollination conditions has not yet been clearly described. In this study, the open-pollinated seeds were collected from 26 mother trees in a 58-year-old seed tree stand. Three seed quality traits, including thousand-seed weight (TSW), germination rate (GR) and germination potential (GP), were measured, and the seeds from eight of 26 families with significant differences in seed quality traits were genotyped through twelve microsatellite markers. In addition, the seeds and sprouts (germinated seeds) from six families were genotyped to reveal the effect of inbreeding on seed germination. The three seed quality traits significantly differed among families (p<0.001). The multilocus outcrossing rate (tm = 0.889) and single-locus outcrossing rate (ts = 0.648) of overall seeds indicated apparent selfing (11.1%) and biparental inbreeding (24.0%). The outcrossing rate in the sprout group (tm = 0.919, ts = 0.788) was higher than that in the seed group (tm = 0.833, ts = 0.646), and the difference in ts between groups was different from zero under the 95% confidence interval (0.024-0.260), suggesting that inbreeding negatively affected seed germination. Linear regression demonstrated that TSW was positively correlated with tm and ts, while GR was negatively related to tm-ts and positively related to ts, implying that seed mass (development) was probably more affected by self-fertilization, but germination capacity was more influenced by biparental inbreeding. Roughly, the inbreeding depression (ID) of TSW was 26.3% with a 0.1 decrease in tm, while GR was 8.4% with a 0.1 decrease in ts. In summary, these results suggest that the IDs during seed development and the germination stage of Masson pine were nonignorable and that more attention should be given to the establishment and management of Masson pine seed production.