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Increasing scientific evidence has demonstrated that the roots of <i>Polygala tenuifolia</i> Willd. have pharmacological effects related to anti-inflammation. Therefore, the aim of this study is to investigate the chemical constituents from <i>P</i>. <i>tenuifolia</i> roots as anti-inflammatory drug candidates. In the present work, twenty-three compounds were isolated from <i>P</i>. <i>tenuifolia</i> roots, including three saponins (<b>1</b>–<b>3</b>), ten phenylpropanoid sucrose esters (<b>4</b>–<b>12</b>), one benzoic acid sugar ester derivative (<b>13</b>), four xanthones (<b>14</b>–<b>17</b>), two hydroxy benzophenone derivatives (<b>18</b> and <b>19</b>), two phenolic derivatives (<b>20</b> and <b>21</b>), and two ionones (<b>22</b> and <b>23</b>). All isolates were tested for their inhibitory effects of LPS-stimulated NO and PGE₂ production in RAW 264.7 macrophages. Among these, 3-<i>O</i>-(3,4,5-trimethoxy-cinnamoyl),6′-<i>O</i>-(<i>p</i>-methoxybenzoyl) sucrose ester (TCMB; <b>11</b>) together with compounds <b>3</b> and <b>21</b> exhibited significant inhibitory effects on NO production, while TCMB and compounds <b>17</b>, <b>19</b>, and <b>21</b> showed strong inhibitory effects on PGE₂ production. Specifically, TCMB (<b>11</b>) downregulated the protein levels of iNOS and COX-2 in LPS-induced RAW 264.7 macrophages. In addition, TCMB (<b>11</b>) dose-dependently diminished the relative mRNA expression levels of iNOS, PGE₂, and proinflammatory cytokines (TNF-α, IL-1β, and IL-6). A molecular docking study showed that TCMB (<b>11</b>) has strong binding affinities with iNOS and COX-2.