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Not knowing the rest of your code or the exact contents it is difficult to offer better advice, but having multiple ifs isn't necessarily a bad thing as long as the code is readable, its not repetitive (each if does distinctly different things), and the code overall does what is expected. But as you seem to always want to return you can add that last, if no Error then normal importModel will be returned.

if (fileCSV == null && fileCSV.ContentLength == 0)
{
    importModel.Error = "Error1";
}
else
{
    List<ImportModel> mappings = _importService.ImportCSVToList<ImportModel>(fileCSV);
    if (mappings.Count > 0)
    {
        IEnumerable<ImportModel> duplicates = mappings.GroupBy(x => x.ProductSku).SelectMany(g => g.Skip(1)).ToList();
        if (duplicates.Any())
        {
            importModel.Error = "Error2";
        }
        else
        {
            var products = _productService.GetProducts(productSkuList).ToList();
            if (!importModel.InvalidSkuList.Any())
            {
                bool isImported = _productService.Import(mappings);
                if (!isImported)
                {
                    importModel.Error = "Error3";
                }
                // should there be a separate Error here or only if !isImported
            }
        }
    }
    else
    {
        importModel.Error =  "Error4";
    }
}
return importModel;