To investigate the effects of long-term fertilization on the accumulation and availability of heavy metals in reddish paddy soil and to analyze the major influencing factors, soil samples were collected after the later rice was harvested in 2018 from a long-term fertilization field experiment that began in 1984. Six treatments were selected, namely CK (control without fertilization), PK (P and K fertilizer), and NPK (N, P, and K fertilizer), and different proportions of organic fertilizer plus chemical fertilizer (M1NPK: 30%M+70%NPK; M2NPK: 50%M+50%NPK; and M3NPK: 70%M+30%NPK), soil chemical properties, total and available heavy metal contents, and the relationships between the available forms of heavy metals and soil chemical parameters and total heavy metals (THM) were analyzed. The results showed that ① long-term fertilization changed the soil chemical properties; compared with those of CK, PK significantly increased the contents of soil available phosphorus (AP) and available potassium (AK), NPK significantly increased the soil organic matter (SOM), cation exchange capacity (CEC), AP, and AK, and the organic fertilizer treatments significantly increased the contents of SOM, CEC, AP, AK, and nitrate (NO3--N). ② There were slight variations in the THM contents under the chemical fertilizer treatments (PK and NPK), whereas the organic fertilizer treatments significantly increased the total contents of Cu, Zn, and Cd. ③ The chemical fertilizer treatments significantly increased the available Cr and As, whereas the organic fertilizer treatments significantly increased the available Cu, Zn, Cr, Cd, As, and Fe. ④ There were significant positive correlations between the available Cu, Zn, Cr, Cd, As, and Fe and the SOM, CEC, AP, and NO3--N. In addition, the available Zn and Cd were significantly positively correlated with the soil pH, whereas the available Pb was significantly negatively correlated with soil pH, SOM, CEC, and NO3--N. ⑤ There were significant positive correlations between the available and total contents of Cu, Zn, and Cd, whereas there were significant negative correlations between the available and total contents of Cr and Fe. ⑥ Redundancy analysis showed that SOM and pH accounted for 80.7% and 5.5% of the variation in THM, whereas the soil CEC, AP, and pH accounted for 81.1%, 4.9%, and 3.3% of the variation in the available heavy metals, respectively. ⑦ The partial least squares path model analysis showed that the path coefficients of the THM, CEC, and AP on the available state of heavy metals were 0.459, 0.417, and 0.293, respectively. Long-term application of organic manure, such as pig manure, significantly improved the soil chemical properties and affected the availability of heavy metals, and soil CEC and AP may play key roles in regulation.