Speciation characteristics of twelve heavy metals in 71 paddy soils from the Jiulong River Basin were analyzed using inductively coupled plasma mass spectrometry (ICP-MS) and the modified BCR protocol. The risk assessment coding method (RAC), ratio of secondary phase and primary phase (RSP), and geoaccumulation index (I) were applied to evaluate the pollution degree of heavy metals in the area. The results show that most of these elements are abundant in the paddy soils and the speciation characteristics of different heavy metals vary. The elements Cd and Mn mainly exist as acid soluble fractions in the soils, with a mean proportion of 46.2% and 35.2%, respectively; Fe and Pb mainly exist as reducible fractions in the soils, with a mean proportion of 64.5% and 41.5%, respectively; and V, Cr, Ni, As, Co, Sr, Zn, and Cu mainly exist as residual fractions in the soils, with a mean proportion of 79.6%, 78.4%, 73.1%, 67.7%, 51.9%, 49.7%, 45.3%, and 38.4%, respectively. The three pollution assessment methods focus on the acid-soluble phase, secondary phase, and total amount of heavy metals, respectively. All have their own application value and disadvantages of incompletion. The comprehensive analysis of these three pollution assessment methods helps to more accurately and comprehensively assess the pollution characteristics of the heavy metals. The results show that the paddy soils are moderately to severely polluted with Cd; the Mn and Sr pollution is mild to severe; the Zn, Pb, Cu, and Co pollution is mild to moderate; the As and Ni pollution is absent or moderate; and V, Fe, and Cr pollution is non-existent or mild.