您可以使用Debug Interface Access SDK来达到您的需求。
特别是MS提供了一个使用IDiaDataSource::loadAndValidateDataFromPdb的示例
来自MS站点的报价：“.pdb文件同时包含签名和期限值。这些值会复制到与.pdb文件匹配的.exe或.dll文件中。在准备数据源之前，此方法将验证已命名的.pdb文件的签名和期限是否与提供的值匹配。”

正如官方文件所说：
符号文件的工作原理
pdb文件包含以下信息：
要在Visual Studio IDE中显示的源文件名和行号。
在应用程序中的何处停止断点。
所以我认为pdb将无法比较它们的源文件是否相同。因为它的内容没有足够的信息。
但是您仍然可以得到一个近似的结果（基于行号和偏移量）。
下面是一个控制台应用程序示例，以满足您的要求（我基于System.Reflection.Metadata）：

using System;
using System.Collections.Generic;
using System.IO;
using System.Reflection.Metadata;
using System.Reflection.Metadata.Ecma335;

class Program
{
    static void Main(string[] args)
    {
        var pdbFile1 = "C:\\Users\\Administrator\\source\\repos\\Blazor-WebAssembly-by-Example\\Chapter09\\ConsoleApp1\\ConsoleApp1.pdb";
        var pdbFile2 = "C:\\Users\\Administrator\\source\\repos\\Blazor-WebAssembly-by-Example\\Chapter09\\ConsoleApp1\\test\\ConsoleApp1.pdb";
        var diff_pdb = "C:\\Users\\Administrator\\source\\repos\\Blazor-WebAssembly-by-Example\\Chapter09\\ConsoleApp1\\bin\\Debug\\net6.0\\ConsoleApp1.pdb";

        var sequencePoints1 = GetSequencePoints(pdbFile1);
        var sequencePoints2 = GetSequencePoints(diff_pdb);

        var areEqual = CompareSequencePoints(sequencePoints1, sequencePoints2);
        Console.WriteLine($"Are sequence points equal: {areEqual}");
    }

    static List<SequencePoint> GetSequencePoints(string pdbFilePath)
    {
        var sequencePoints = new List<SequencePoint>();

        using (var stream = File.OpenRead(pdbFilePath))
        {
            var pdbReaderProvider = MetadataReaderProvider.FromPortablePdbStream(stream);
            var pdbReader = pdbReaderProvider.GetMetadataReader();
            foreach (var methodDebugHandle in pdbReader.MethodDebugInformation)
            {
                var methodDebugInformation = pdbReader.GetMethodDebugInformation(methodDebugHandle);
                var sequencePointsForMethod = methodDebugInformation.GetSequencePoints();
                sequencePoints.AddRange(sequencePointsForMethod);
            }
        }

        return sequencePoints;
    }

    static bool CompareSequencePoints(List<SequencePoint> sequencePoints1, List<SequencePoint> sequencePoints2)
    {
        if (sequencePoints1.Count != sequencePoints2.Count)
        {
            return false;
        }

        for (int i = 0; i < sequencePoints1.Count; i++)
        {
            if (sequencePoints1[i].StartLine != sequencePoints2[i].StartLine ||
                sequencePoints1[i].EndLine != sequencePoints2[i].EndLine ||
                sequencePoints1[i].Offset != sequencePoints2[i].Offset)
            {
                return false;
            }
        }

        return true;
    }
}

字符串
上面的代码应该可以直接运行。